Bioaugmentation of Exogenous Strain Rhodococcus sp. 2G Can Efficiently Mitigate Di(2-ethylhexyl) Phthalate Contamination to Vegetable Cultivation

Simultaneously degradation of various phthalate esters by Rhodococcus sp. AH-ZY2: Strain, omics and enzymatic study

Phthalate esters (PAEs) are widely used as plasticizers and cause serious complex pollution problem in environment. Thus, strains with efficient ability to simultaneously degrade various PAEs are required. In this study, a newly isolated strain Rhodococcus sp. AH-ZY2 can degrade 500 mg/L Di-n-octyl phthalate completely within 16 h and other 500 mg/L PAEs almost completely within 48 h at 37 °C, 180 rpm, and 2 % (v/v) inoculum size of cultures with a OD600 of 0.8. OD600 = 0.8, 2 % (v/v). Twenty genes in its genome were annotated as potential esterase and four of them (3963, 4547, 5294 and 5359) were heterogeneously expressed and characterized. Esterase 3963 and 4547 is a type I PAEs esterase that hydrolyzes PAEs to phthalate monoesters. Esterase 5294 is a type II PAEs esterase that hydrolyzes phthalate monoesters to phthalate acid (PA). Esterase 5359 is a type III PAEs esterase that simultaneously degrades various PAEs to PA. Molecular docking results of 5359 suggested that the size and indiscriminate binding feature of spacious substrate binding pocket may contribute to its substrate versatility. AH-ZY2 is a potential strain for efficient remediation of PAEs complex pollution in environment. It is first to report an esterase that can efficiently degrade mixed various PAEs.

Efficient remediation of di-(2-ethylhexyl) phthalate and plant-growth promotion with the application of a phosphate-solubilizing compound microbial agent

The ecotoxic endocrine-disrupting chemical di-(2-ethylhexyl) phthalate (DEHP) is ubiquitous in agricultural soil, posing a serious threat to human health. Here, we report efficient soil-borne DEHP degradation and plant growth promotion by a microbial organic fertilizer GK-PPB prepared by combining a recycled garden waste-kitchen waste compost product with ternary compound microbial agent PPB-MA, composed of Penicillium oxalic MB08F, Pseudomonas simiae MB751, and Bacillus tequilensis MB05B. The combination of MB08F and MB751 provided synergistic phosphorus solubilization, and MB05B enhanced the DEHP degradation capacity of MB08F via bioemulsification. Under optimal conditions (25.70 °C and pH 7.62), PPB-MA achieved a 96.81 % degradation percentage for 1000 mg L-1 DEHP within 5 days. The degradation curve followed first-order kinetics with a half-life of 18.24 to 24.76 h. A complete mineralization pathway was constructed after identifying the degradation intermediates of 2H-labeled DEHP. Evaluation in Caenorhabditis elegans N2 showed that PPB-MA eliminated the ecological toxicity of DEHP. A pakchoi (Brassica chinensis L.) pot experiment demonstrated that GK-PPB promoted phosphorus solubilization and plant growth, reduced soil DEHP residue, and decreased DEHP accumulation in pakchoi, suggesting its potential practical utility in environmentally responsible and safe cultivation of vegetables.

Degradation of petroleum hydrocarbon contaminants by Rhodococcus erythropolis KB1 synergistic with alfalfa (Medicago sativa L.)

Petroleum hydrocarbons are a stubborn pollutant that is difficult to degrade globally, and plant-microbial degradation is the main way to solve this type of pollutant. In this study, the physiological and ecological responses of alfalfa to petroleum hydrocarbons in different concentrations of petroleum hydrocarbon-contaminated soil with KB1 (Rhodococcus erythropolis) were analyzed and determined by laboratory potting techniques. The growth of alfalfa (CK) and alfalfa with KB1 (JZ) in different concentrations of petroleum hydrocarbons contaminated soil was compared and analyzed. The results of the CK group showed that petroleum hydrocarbons could significantly affect the activity of alfalfa antioxidant enzyme system, inhibit the development of alfalfa roots and the normal growth of plants, especially in the high-concentration group. KB1 strain had the ability to produce IAA, form biofilm, fix nitrogen, produce betaine and ACC deaminase, and the addition of KB1 could improve the growth traits of alfalfa in the soil contaminated with different concentrations of petroleum hydrocarbons, the content of soluble sugars in roots, and the stress resistance and antioxidant enzyme activities of alfalfa. In addition, the degradation kinetics of the strain showed that the degradation rate of petroleum could reach 75.2% after soaking with KB1. Furthermore, KB1 can efficiently degrade petroleum hydrocarbons in advance and significantly alleviate the damage of high concentration of petroleum hydrocarbons to plant roots. The results showed that KB1 strains and alfalfa plants could effectively enhance the degradation of petroleum hydrocarbons, which provided new ideas for improving bioremediation strategies.

Dibutyl phthalate degradation by Paenarthrobacter ureafaciens PB10 through downstream product myristic acid and its bioremediation potential in contaminated soil

Dibutyl phthalate (DBP) is a widely used plasticizer to make plastic flexible and long-lasting. It is easily accessible in a broad spectrum of environments as a result of the rising level of plastic pollution. This compound is considered a top-priority toxicant and persistent organic pollutant by international environmental agencies for its endocrine disruptive and carcinogenic propensities. To mitigate the DBP in the soil, one DBP-degrading bacterial strain was isolated from a plastic-polluted landfill and identified as Paenarthrobacter ureafaciens PB10 by 16S rRNA gene sequence-based homology. The strain was found to develop a distinct transparent halo zone around grown colonies on an agar plate supplemented with DBP. The addition of yeast extract (100 mg/L) as a nutrient source accelerated cell biomass production and DBP degradation rate; however, the presence of glucose suppressed DBP degradation by the PB10 strain without affecting its ability to proliferate. The strain PB10 was efficient in eliminating DBP under various pH conditions (5.0-8.0). Maximum cell growth and degradation of 99.49% at 300 mg/L DBP were achieved in 72 h at the optimized mineral salt medium (MS) conditions of pH 7.0 and 32 °C. Despite that, when the concentration of DBP rose to 3000 mg/L, the DBP depletion rate was measured at 79.34% in 72 h. Some novel intermediate metabolites, like myristic acid, hexadecanoic acid, stearic acid, and the methyl derivative of 4-hydroxyphenyl acetate, along with monobutyl phthalate and phthalic acid, were detected in the downstream degradation process of DBP through GC-MS profiling. Furthermore, in synchronization with native soil microbes, this PB10 strain successfully removed a notable amount of DBP (up to 54.11%) from contaminated soil under microcosm study after 10 d. Thus, PB10 has effective DBP removal ability and is considered a potential candidate for bioremediation in DBP-contaminated sites.

Status of phthalate esters pollution in facility agriculture across China: Spatial distribution, risk assessment, and remediation measures

The pervasive utilization of phthalate esters (PAEs) in plastic products has led to an emergent concern regarding the PAEs contamination in environmental matrices. However, the overall understanding of PAEs pollution in facility agriculture and its relevant risks remain limited. In this paper, the characteristics, health risks, and remediation measures of PAEs pollution in facility agriculture across China were analyzed. In general, PAEs pollution in facility agriculture soil in SWC and vegetables in SC were more serious than that in the other six regions (p < 0.05). The total level of six PAEs ranged from 0.053 to 5.663 mg·kg-1 in soil samples, nd (not detectable) to 12.540 mg·kg-1 in vegetable samples, with mean values of 0.951 mg·kg-1 and 2.458 mg·kg-1, respectively. DEHP and DnBP were dominant in both soil and vegetable samples with a total contribution of over 70 % of the six PAEs, but their concentrations were a little lower in soil samples. The PAEs concentrations of leafy, root, and fruit vegetables exhibited a descending trend. Correlation analysis revealed that the relationships between soil and vegetable PAEs concentrations remained inconclusive, lacking clear correlations. Furthermore, risk assessments indicated that the hazard quotient (HQ) for both total and individual PAEs in the vast majority of vegetable samples remained within acceptable thresholds. Meanwhile, all values for carcinogenic risks (CR) were confined within the range of 10-4. In conclusion, the study outlines remediation measures aimed at precluding and mitigating the environmental risks associated with PAEs exposure. These findings furnish a scientific foundation for the targeted assessment and judicious management of PAEs pollution within facility agriculture landscape of China.

Synthetic bacterial consortia enhanced the degradation of mixed priority phthalate ester pollutants

Dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), butyl benzyl phthalate (BBP), bis(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DOP) are hazardous chemicals listed as priority pollutants that disrupt endocrine systems. According to available reports, these six priority phthalate esters (PAEs) are considered the most polluting; however, no studies have been conducted on the efficient remediation of these PAEs. We therefore designed and constructed a synthetic bacterial consortium capable of the simultaneous and efficient degradation of six priority PAEs in minimal inorganic salt medium (MSM) and soil. The consortium comprised Glutamicibacter sp. ZJUTW, which demonstrates priority for degrading short-chain PAEs; Cupriavidus sp. LH1, which degrades phthalic acid (PA) and protocatechuic acid (PCA), intermediates of the PAE biodegradation process; and Gordonia sp. GZ-YC7, which efficiently degrades long-chain priority PAEs, including DEHP and DOP. In MSM containing the six mixed PAEs (250 mg/L each), the ZJUTW + YC + LH1 consortium completely degraded the four short-chain PAEs within 48 h, and DEHP (100%) and DOP (62.5%) within 72 h. In soil containing the six mixed PAEs (DMP, DEP, BBP, and DOP, 400 mg/kg each; DBP and DEHP, 500 mg/kg, each), the ZJUTW + YC + LH1 consortium completely degraded DMP, DEP, BBP, and DBP within 6 days, and 70.84% of DEHP and 66.24% of DOP within 2 weeks. The consortium efficiently degraded the six mixed PAEs in both MSM and soil. We thus believe that this synthetic microbial consortium is a strong candidate for the bioremediation of environments contaminated with mixed PAE pollutants.

Substrate-enzyme interactions and catalytic mechanism in a novel family VI esterase with dibutyl phthalate-hydrolyzing activity

Microbial degradation has been confirmed as effective and environmentally friendly approach to remediate phthalates from the environment, and hydrolase is an effective element for contaminant degradation. In the present study, a novel dibutyl phthalate (DBP)-hydrolyzing carboxylesterase (named PS06828) from Pseudomonas sp. PS1 was heterogeneously expressed in E. coli, which was identified as a new member of the lipolytic family VI. Purified PS06828 could efficiently degrade DBP with a wide range of temperature (25-37 °C) and pH (6.5-9.0). Multi-spectroscopy methods combined with molecular docking were employed to study the interaction of PS06828 with DBP. Fluorescence and UV-visible absorption spectra revealed the simultaneous presence of static and dynamic component in the fluorescence quenching of PS06828 by DBP. Synchronous fluorescence and circular dichroism spectra showed inconspicuous alteration in micro-environmental polarity around amino acid residues but obvious increasing of α-helix and reducing of β-sheet and random coil in protein conformation. Based on the information on exact binding sites of DBP on PS06828 provided by molecular docking, the catalytic mechanism mediated by key residues (Ser113, Asp166, and His197) was proposed and subsequently confirmed by site-directed mutagenesis. The results can strengthen our mechanistic understanding of family VI esterase involved in hydrolysis of phthalic acid esters, and provide a solid foundation for further enzymatic modification.

Divergence in the distribution of di(2-ethylhexyl) phthalate (DEHP) in two soils

Understanding the distribution of di(2-ethylhexyl) phthalate (DEHP) is necessary for future risk evaluation of DEHP in agricultural soils. This study used 14C-labeled DEHP to examine its volatilization, mineralization, extractable residues, and non-extractable residues (NERs) incubated in Chinese typical red and black soil with/without Brassica chinensis L. Results showed that after incubated for 60 days, 46.3% and 95.4% of DEHP were mineralized or transformed into NERs in red and black soil, respectively. The distribution of DEHP in humic substances as NER descended in order: humin > fulvic acids > humic acids. DEHP in black soil was more bioavailable, with 6.8% of initial applied radioactivity left as extractable residues at the end of incubation when compared with red soil (54.5%). Planting restrained the mineralization of DEHP by 18.5% and promoted the extractable residues of DEHP by 1.5% for black soil, but no such restrain was observed in red soil. These findings provide valuable information for understanding the distribution of DEHP in different soils and develop the understanding for the risk assessments of PAEs in typical soils.

Complete genome of Mycolicibacterium phocaicum RL-HY01, a PAEs-degrading marine bacterial strain isolated from Zhanjiang Bay, China

Mycolicibacterium phocaicum RL-HY01, a marine bacterial strain with the capability to degrade phthalic acid esters (PAEs), was isolated from Zhanjiang Bay, China. Here, the complete genome sequence of strain RL-HY01 was presented. The genome of strain RL-HY01 contains one circular chromosome of 6,064,759 bp with a G + C content of 66.93 mol%. The genome contains 5681 predicted protein-encoding genes, 57 tRNA genes, and 6 rRNA genes. Genes and gene clusters potentially involved in the metabolism of PAEs were further identified. The genome Mycolicibacterium phocaicum RL-HY01 will be helpful for advancing our understanding of the fate of PAEs in marine ecosystem.

Evaluation of distinct molecular architectures and coordinated regulation of the catabolic pathways of oestrogenic dioctyl phthalate isomers in Gordonia sp

Bacterial strain GONU, belonging to the genus Gordonia, was isolated from a municipal waste-contaminated soil sample and was capable of utilizing an array of endocrine-disrupting phthalate diesters, including di-n-octyl phthalate (DnOP) and its isomer di(2-ethylhexyl) phthalate (DEHP), as the sole carbon and energy sources. The biochemical pathways of the degradation of DnOP and DEHP were evaluated in strain GONU by using a combination of various chromatographic, spectrometric and enzymatic analyses. Further, the upregulation of three different esterases (estG2, estG3 and estG5), a phthalic acid (PA)-metabolizing pht operon and a protocatechuic acid (PCA)-metabolizing pca operon were revealed based on de novo whole genome sequence information and substrate-induced protein profiling by LC-ESI-MS/MS analysis followed by differential gene expression by real-time PCR. Subsequently, functional characterization of the differentially upregulated esterases on the inducible hydrolytic metabolism of DnOP and DEHP revealed that EstG5 is involved in the hydrolysis of DnOP to PA, whereas EstG2 and EstG3 are involved in the metabolism of DEHP to PA. Finally, gene knockout experiments further validated the role of EstG2 and EstG5, and the present study deciphered the inducible regulation of the specific genes and operons in the assimilation of DOP isomers.

Endophytic Phthalate-degrading Bacillus subtilis N-1-gfp colonizing in soil-crop system shifted indigenous bacterial community to remove di-n-butyl phthalate

Endophytic bacteria can degrade toxic phthalate (PAEs). Nevertheless, the colonization and function of endophytic PAE-degrader in soil-crop system and their association mechanism with indigenous bacteria in PAE removal remain unknown. Here, endophytic PAE-degrader Bacillus subtilis N-1 was marked with green fluorescent protein gene. Inoculated strain N-1-gfp could well colonize in soil and rice plant exposed to di-n-butyl phthalate (DBP) as directly confirmed by confocal laser scanning microscopy and realtime PCR. Illumina high-throughput sequencing demonstrated that inoculated N-1-gfp shifted indigenous bacterial community in rhizosphere and endosphere of rice plants with significant increasing relative abundance of its affiliating genus Bacillus than non-inoculation. Strain N-1-gfp exhibited efficient DBP degradation with 99.7% removal in culture solutions, and significantly promoted DBP removal in soil-plant system. Strain N-1-gfp colonization help plant enrich specific functional bacteria (e.g., pollutant-degrading bacteria) with significant higher relative abundances and stimulated bacterial activities (e.g., pollutant degradation) compared with non-inoculation. Furthermore, strain N-1-gfp displayed strong interaction with indigenous bacteria for accelerating DBP degradation in soil, decreasing DBP accumulation in plants and promoting plant growth. This is the first report on well colonization of endophytic DBP-degrader Bacillus subtilis in soil-plant system and its bioaugmentation with indigenous bacteria for promoting DBP removal.

Adaptation of bacterial community in maize rhizosphere for enhancing dissipation of phthalic acid esters in agricultural soil

Rhizospheric degradation is a green and in situ strategy to accelerate dissipation of organic pollutants in soils. However, the mechanism on microbial degradation of phthalic acid esters (PAEs) in rhizosphere is still unclear. Here, the bacterial community and function genes in bulk and rhizospheric soils of maize (Zea mays L.) exposed to gradient concentrations of di-(2-ethylhexyl) phthalate (DEHP) were analyzed with 16 S rRNA, metagenomic sequencing and quantitative PCR (qPCR). Maize rhizosphere significantly increased the dissipation of DEHP by 4.02-11.5% in comparison with bulk soils. Bacterial community in rhizosphere exhibited more intensive response and shaped its beneficial structure and functions to DEHP stress than that in bulk soils. Both rhizospheric and pollution effects enriched more PAE-degrading bacteria (e.g., Bacillus and Rhizobium) and function genes in rhizosphere than in bulk soil, which played important roles in degradation of PAEs in rhizosphere. The PAE-degrading bacteria (including genera Sphingomonas, Sphingopyxis and Lysobacter) identified as keystone species participated in DEHP biodegradation. Identification of PAE intermediates and metagenomic reconstruction of PAE degradation pathways demonstrated that PAE-degrading bacteria degraded PAEs through cooperation with PAE-degrading and non-PAE-degrading bacteria. This study provides a comprehensive knowledge for the microbial mechanism on the superior dissipation of PAEs in rhizosphere.

Phthalates - A family of plasticizers, their health risks, phytotoxic effects, and microbial bioaugmentation approaches

Phthalates are a family of reprotoxicant compounds, predominantly used as a plasticizer to improve the flexibility and longevity of consumable plastic goods. After their use these plastic products find their way to the waste disposal sites where they leach out the hazardous phthalates present within them, into the surrounding environment, contaminating soil, groundwater resources, and the nearby water bodies. Subsequently, phthalates move into the living system through the food chain and exhibit the well-known phenomenon of biological magnification. Phthalates as a primary pollutant have been classified as 1B reprotoxicants and teratogens by different government authorities and they have thus imposed restrictions on their use. Nevertheless, the release of these compounds in the environment is unabated. Bioremediation has been suggested as one of the ways of mitigating this menace, but studies regarding the field applications of phthalate utilizing microbes for this purpose are limited. Through this review, we endeavor to make a deeper understanding of the cause and concern of the problem and to find out a possible solution to it. The review critically emphasizes the various aspects of phthalates toxicity, including their chemical nature, human health risks, phytoaccumulation and entry into the food chain, microbial role in phthalate degradation processes, and future challenges.

The efficient persistence and migration of Cupriavidus gilardii T1 contribute to the removal of MCPA in laboratory and field soils

The application of exogenous biodegradation strains in pesticide-polluted soils encounters the challenges of migration and persistence of inoculants. In this study, the degradation characteristics, vertical migration capacity, and microbial ecological risk assessment of an enhanced green fluorescent protein (EGFP)-tagged 2-Methyl-4-chlorophenoxyacetic acid (MCPA)-degrading strain Cupriavidus gilardii T1 (EGFP) were investigated in the laboratory and field soils. The optimum remediation conditions for T1 (EGFP) was characterized in soils. Meanwhile, leaching experiments showed that T1 (EGFP) migrated vertically downwards in soil and contribute to the degradation of MCPA at different depths. After inoculation with T1 (EGFP), a high expression levels of EGFP gene was observed at 28 d in the laboratory soil and at 45 d in the field soil. The degradation rates of MCPA were ≥ 60% in the laboratory soil and ≥ 48% in the field soil, indicating that T1 (EGFP) can efficiently and continuously remove MCPA in both laboratory and field conditions. In addition, the inoculation of T1 (EGFP) not only showed no significant impact on the soil microbial community structure but also can alleviate the negative effects induced by MCPA to some extent. Overall, our findings suggested that T1 (EGFP) strain is an ecologically safe resource for the in situ bioremediation of MCPA-contaminated soils.

Uptake pathways of phthalates (PAEs) into Chinese flowering cabbage grown in plastic greenhouses and lowering PAE accumulation by spraying PAE-degrading bacterial strain

Uptake pathway and accumulation variation of soil and airborne phthalates (PAEs) in plastic greenhouses by vegetables remains unclear. Here, pot experiments of Chinese flowering cabbage were designed to distinguish root or leaf uptake pathways of PAEs, and investigate the mitigation of spraying PAE-degrading strain in PAE accumulation by vegetables. The results showed that leaves of Chinese flowering cabbage grown in plastic greenhouses absorbed more PAEs from air than those of outside greenhouses. Airborne PAEs were mainly stored in leaf surfaces of vegetables grown inside greenhouse, while PAEs absorbed by roots from soil were translocated and mainly stored in mesophyll, especially in cell walls and organelles. PAE concentrations in mesophyll elevated with increasing soil PAE levels, whereas those in leaf surfaces were not influenced by soil PAE levels. The values of bioconcentration factors for leaves inside greenhouses were significantly (1.39-3.47 fold) higher than those outside. PAE-degrading strain (Rhodococcus pyridinivorans XB) sprayed on leaf surfaces could grow well and Rhodococcus was the dominant genus as confirmed by Illumina high-throughput sequencing. PAE-degrading strain effectively reduced PAEs by 12.9%-34.9% in leaf surface, but not those in vegetables grown in high-PAE soil. This study demonstrated mitigation of spraying PAE-degrading strain in PAE accumulation by vegetable leaves from air of plastic greenhouse.

Spatial distribution model of DEHP contamination categories in soil based on Bi-LSTM and sparse sampling

Soil pollution is a serious threat to human life and development. Different remedial measures are applied to soils with different levels of contamination. The degree of soil contamination in different areas is generally evaluated and categorised based on the analysis of samples. Regional soil sampling sites are generally sparse because of the cost of sampling and other factors, which makes it difficult to accurately assess the extent of regional soil contamination. In this study, a spatial classification model was established for the Di(2-ethylhexyl) phthalate (DEHP) pollution level using a Bi-directional Long Short-Term Memory (Bi-LSTM) neural network considering that the sampling information gradually diminishes with increasing distance between the sampling and prediction points. In this study, a method is proposed for the prediction of the spatial distribution of soil pollution categories based on sparse samples. We also established a model for the spatial distribution of organic pollution categories. The analysis of an actual contaminated area shows that the DEHP concentrations at different locations can be effectively predicted with the proposed method by categorising the contamination levels of specific DEHP samples. The results show that the method can be used to classify the degree of light/severe DEHP contamination. The results are in good agreement with the actual situation, verifying the validity of the method. This method is important for the rapid assessment of the spatial distribution of soil contamination levels based on sparse sampling.

Phthalic acid esters degradation by a novel marine bacterial strain Mycolicibacterium phocaicum RL-HY01: Characterization, metabolic pathway and bioaugmentation

Phthalic acid esters (PAEs) are one of the most widely used plasticizers and the well-studied environmental pollutants with endocrine disrupting properties. Investigation about PAEs in terrestrial ecosystem has been extensively conducted while the fate of PAEs in marine environment remains underexplored. In this study, a novel di-(2-ethylhexyl) phthalate (DEHP) degrading marine bacterial strain, Mycolicibacterium phocaicum RL-HY01, was isolated and characterized from intertidal sediments. Strain RL-HY01 could utilize a range of PAE plasticizers as sole carbon source for growth. The effects of different environmental factors on the degradation of PAEs were evaluated and the results indicated that strain RL-HY01 could efficiently degrade PAEs under a wide range of pH (5.0 to 9.0), temperature (20 °C to 40 °C) and salinity (below 10%). Specifically, when Tween-80 was added as solubilizing agent, strain RL-HY01 could rapidly degrade DEHP and achieve complete degradation of DEHP (50 mg/L) in 48 h. The kinetics of DEHP degradation by RL-HY01 were well fitted with the modified Gompertz model. The metabolic intermediates of DEHP by strain RL-HY01 were identified by ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis and then the metabolic pathway of DEHP was deduced. DEHP was transformed into di-ethyl phthalate (DEP) via β-oxidation and then DEP was hydrolyzed into phthalic acid (PA) by de-esterification. PA was further transformed into gentisate via salicylic acid and further utilized for cell growth. Bioaugmentation of strain RL-HY01 with marine samples was performed to evaluate its application potential and the results suggested that strain RL-HY01 could accelerate the elimination of DEHP in marine samples. The results have advanced our understanding of the fate of PAEs in marine ecosystem and identified an efficient bioremediation strategy for PAEs-polluted marine sites.

Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.

Rapidly degradation of di-(2-ethylhexyl) phthalate by Z-scheme Bi2O3/TiO2@reduced graphene oxide driven by simulated solar radiation

Di(2-ethylhexyl) phthalate (DEHP) is a priority environmental pollutant with carcinogenic, teratogenic, and mutagenic toxicity. Because it is widely used and ubiquitous in water, it is urgent to use a non-toxic, fast, and non-temperature dependent photocatalyst for degradation. Herein, a Z-scheme heterojunction composite catalyst consisting of Bi₂O₃ and TiO₂ with reduced graphene oxide (rGO) as a two-dimensional template was designed and characterized. Under simulated solar radiation, the catalyst doped with 4% rGO presented the best photocatalytic DEHP (10 mg L^-1) degradation at pH = 6, reaching 89% conversion in 90 min, and the degradation rate was 2.05 times higher than unmodified materials. The successful preparation of the Z-scheme junction enhanced the utilization of visible light region, thereby improving the DEHP's photocatalytic degradation performance. Subsequently, density functional theory (DFT) combined with GC-MS metabolite detection to propose a complete DEHP photocatalytic degradation mechanism. ·O₂^- and ·OH were detected as the primary reactive oxygen radicals involved in DEHP degradation, which easily attacked the O11 site with a high Fukui index (f⁰) through de-esterification, β-oxidation, and hydroxylation. While satisfying the rapid degradation, the highly repeatable catalyst cleaved the aromatic ring so that DEHP achieved mineralization during the degradation process. Therefore, its ability to completely degrade was very promising for environmental remediation, especially in water treatment. Besides, there were only a few studies on the degradation mechanism and reaction pathway of DEHP under visible light, which provided a theoretical basis for the aromatic compounds' photocatalysis research.

Remediation strategies for mitigation of phthalate pollution: Challenges and future perspectives

Phthalates are a group of emerging xenobiotic compounds commonly used as plasticizers. In recent times, there has been an increasing concern over the risk of phthalate exposure leading to adverse effects to human health and the environment. Therefore, it is necessary to not only understand the current status of phthalate pollution, their sources, exposure routes and health impacts, but also identify remediation technologies for mitigating phthalate pollution. Present review article aims to inform its readers about the ever increasing data on health burdens posed by phthalates and simultaneously highlights the recent advancements in research to alleviate phthalate contamination from environment. The article enumerates the major phthalates in use today, traces their environmental fate, addresses their growing health hazard concerns and largely focus on to provide an in-depth understanding of the different physical, chemical and biological treatment methods currently being used or under research for alleviating the risk of phthalate pollution, their challenges and the future research perspectives.

Mechanistic insight into esterase-catalyzed hydrolysis of phthalate esters (PAEs) based on integrated multi-spectroscopic analyses and docking simulation

A novel PAE-hydrolyzing esterase (named Hyd) gene was screened from the genomic library of Rhodococcus sp. 2G and was successfully expressed in heterologous E. coli, which was defined as a new family of esterolytic enzymes. The purified Hyd could efficiently degrade various PAEs, displaying high activity and stability with a broad range of pH (4-10) and temperature (20-60 °C). Interaction mechanism of Hyd with dibutyl phthalate (DBP) was investigated by integrated multi-spectroscopic and docking simulation methods. Fluorescence and UV-vis spectra revealed that DBP could quench the fluorescence of Hyd through a static quenching mechanism. The results from synchronous fluorescence and CD spectra confirmed that the DBP binding to Hyd triggered conformational and micro-environmental changes of Hyd, which were characterized by increased stretching extent and random coil, and decreased α-helix and β-sheet. Molecular docking study showed that DBP could be bound to the cavity of Hyd with hydrogen bonding and hydrophobic interaction. A novel and distinctive catalytic mechanism was proposed: two key residues Thr¹⁹⁰ and Ser¹⁹¹ might catalyze the hydrolysis of DBP, instead of the conserved catalytic triad (Ser-His-Asp) reported elsewhere, which was confirmed by site-directed mutagenesis.

Enhancing the activity and thermal stability of a phthalate-degrading hydrolase by random mutagenesis

Our previous work has reported that EstJ6 was a phthalate-degrading hydrolase. In the study, a random mutant library was constructed by two rounds of error-prone PCR, three mutants (ET1.1, ET2.1, and ET2.2) with enhanced hydrolytic activity against dibutyl phthalate (DBP) were obtained. The best mutant ET2.2, accumulated three amino acid substitutions (Thr91Met, Ala67Val, and Val249Ile) and exhibited 2.8-fold increase enzyme activity and 2.3-fold higher expression level. Meanwhile, compared with EstJ6, ET2.2 showed over 50% improvement in thermostability (at 50 °C for 1 h) and 1.2-fold increase in 50% methanol tolerance. Kinetic parameters analysis revealed that the Km value for ET2.2 decreased by 60% and the kcat/Km value increased by 166%. The molecular docking indicated that the shortening of hydrogen bond between Ser146-OH and DBP-CO, which may led to an increase in enzyme activity and catalytic efficiency, the enhancement of hydrophobicity of hydrophobic pocket was related to the improvement of organic solvents tolerance, and three hydrophobic amino acid substitutions Thr91Met, Ala67Val, and Val249Ile facilitated to improve the thermal stability and organic solvents tolerance. These results confirmed that random mutagenesis was an effective tool for improving enzyme properties and lay a foundation for practical applications of phthalate-degrading hydrolase in biotechnology and industrial fields.

Enhanced uptake of di-(2-ethylhexyl) phthalate by the influence of citric acid in Helianthus annuus cultivated in artificially contaminated soil

Di-(2-ethylhexyl) phthalic acid (DEHP) is the most extensively practiced plasticizer compound and a representative endocrine disrupting pollutant. Recently, the environmental impact and toxicological causes of DHEP on human health have been extensively investigated. DEHP uptake by plants is most significant biotransformation process of DEHP in environment. In this study, Helianthus annuus (H.annuus), vastly efficient in phytoremediation of polluted soil was selected to study the uptake and phytoremediation of DEHP in contaminated soil. In addition, the effect of citric acid on enhanced uptake and removal of DEHP was also investigated. The orders of biomass concentrations showed in the CA treatments were 200 mM (60.5 g) ˃ 150 mM (54.5) ˃ 100 mM (50.2 g) ˃ 50 mM (46.5 g). The maximum shoot accumulation of DHEP (20 mg/kg) was observed at 200 mM citric acid treatment compared to all other treatments (50, 100, and 150 mM). Significant difference of the antioxidant enzymes activity (CAT, 25.7, POD, 22.5 (μmol H₂O₂/min/g FW) and COD 5.6 U/g FW) was observed between control and CA treatments as well as different concentrations of CA treated plants. The maximum ALP (0.17 mg.g^-1soil.24 h^-1) and urease activities (1.65 mg.g^-1soil.24 h^-1) were observed at 200 mM CA amended soils. The application of citric acid was significantly enhanced the H.annuus growth as well as uptake of DEHP. The results explored that the citric acid has excellent potential for the enhanced uptake of DEHP in contaminated soil.

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.

High-effectively degrade the di-(2-ethylhexyl) phthalate via biochemical system: Resistant bacterial flora and persulfate oxidation activated by BC@Fe3O4

Di-(2-ethylhexyl) phthalate (DEHP) has been classified as a priority pollutant which increased the healthy risk to human and animals dramatically. Hence, a novel biochemical system combined by DEHP-resistant bacterial flora (B) and a green oxidant of persulfate (PS) activated by Nano-Fe₃O₄ was applied to degrade DEHP in contaminated soil. In this study, the resistant bacterial flora was screened from activated sludge and immobilized by sodium alginate (SAB). Nano-Fe₃O₄ was coated on biochar (BC@Fe₃O₄) to prevent agglomerating in soil. X-ray diffraction (XRD) and scanning electron microscope (SEM) were utilized to characterize BC@Fe₃O₄. Results demonstrated that the treatment of biochemical system (SAB + BC@Fe₃O₄ + PS) presented the maximum degradation rate about 92.56% within 24 days of incubation and improved soil microecology. The 16S rDNA sequences analysis of soil microorganisms showed a significantly different abundance and a similar diversity among different treatments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional genes difference analysis showed that some metabolic pathways, such as metabolism of cofactors and vitamins, energy metabolism, cell growth and death, replication and repair, were associated with the biodegradation of DEHP. Besides, DEHP was converted to MEHP and PA by biodegradation, while DEHP was converted to DBP and PA by persulfate and BC@Fe₃O₄, and then ultimately degraded to CO₂ and H₂O.

Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view

This study aims to clarify the interaction mechanism of substrate with catechol 2,3-dioxygenase (C23O) through multi-technique combination. A novel C23O (named C23O-2G) was cloned, heterogeneously expressed, and identified as a new member in subfamily I.2 of extradiol dioxygenases. Based on the simulations of molecular docking and dynamics, the exact binding sites of catechol on C23O-2G were identified, and the catalytic mechanism mediated by key residues was proposed. The roles of the predicted residues during catalysis were confirmed by site-directed mutagenesis, and the mutation of Thr254 could significantly increase catalytic efficiency and substrate specificity of C23O-2G. The binding and thermodynamic parameters obtained from fluorescence spectra suggested that catechol could effectively quench the intrinsic fluorescence of C23O-2G via static and dynamic quenching mechanisms and spontaneously formed C23O-2G/catechol complex by the binding forces of hydrogen bond and van der Waals force. The results of UV-vis spectra, synchronous fluorescence, and CD spectra revealed obvious changes in the microenvironment and conformation of C23O-2G, especially for the secondary structure. The atomic force microscope images further demonstrated the changes from an appearance point of view. This study could improve our mechanistic understanding of representative dioxygenases involved in aromatic compound degradation.

Identification and characterization of a novel phthalate-degrading hydrolase from a soil metagenomic library

Phthalate esters have raised public concerns owing to their effects on the environment and human health. We identified a novel phthalate-degrading hydrolase, EstJ6, from a metagenomic library using function-driven screening. Phylogenetic analysis indicated that EstJ6 is a member of family IV esterases. EstJ6 hydrolyzed various dialkyl and monoalkyl phthalate esters, and exhibited high hydrolytic activity (128 U/mg) toward dibutyl phthalate at 40 °C and pH 7.5. EstJ6 hydrolyzed not only common phthalate esters with simple side chains but also diethylhexyl phthalate and monoethylhexyl phthalate, which have complex and long side chains. Site-directed mutagenesis indicated that the catalytic triad residues of EstJ6 consists of Ser146, Glu240, and His270. EstJ6 is therefore a promising biodegradation enzyme, and our study illustrates the advantages of a metagenomic approach in identifying enzyme-coding genes for agricultural, food, and biotechnological applications.