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Nagy KK, Takács K, Németh I, Varga B, Grolmusz V, Molnár M, Vértessy BG. Novel enzymes for biodegradation of polycyclic aromatic hydrocarbons identified by metagenomics and functional analysis in short-term soil microcosm experiments. Sci Rep 2024; 14:11608. [PMID: 38773163 PMCID: PMC11109138 DOI: 10.1038/s41598-024-61566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic substances. On soils contaminated with PAHs, crop cultivation, animal husbandry and even the survival of microflora in the soil are greatly perturbed, depending on the degree of contamination. Most microorganisms cannot tolerate PAH-contaminated soils, however, some microbial strains can adapt to these harsh conditions and survive on contaminated soils. Analysis of the metagenomes of contaminated environmental samples may lead to discovery of PAH-degrading enzymes suitable for green biotechnology methodologies ranging from biocatalysis to pollution control. In the present study, our goal was to apply a metagenomic data search to identify efficient novel enzymes in remediation of PAH-contaminated soils. The metagenomic hits were further analyzed using a set of bioinformatics tools to select protein sequences predicted to encode well-folded soluble enzymes. Three novel enzymes (two dioxygenases and one peroxidase) were cloned and used in soil remediation microcosms experiments. The experimental design of the present study aimed at evaluating the effectiveness of the novel enzymes on short-term PAH degradation in the soil microcosmos model. The novel enzymes were found to be efficient for degradation of naphthalene and phenanthrene. Adding the inorganic oxidant CaO2 further increased the degrading potential of the novel enzymes for anthracene and pyrene. We conclude that metagenome mining paired with bioinformatic predictions, structural modelling and functional assays constitutes a powerful approach towards novel enzymes for soil remediation.
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Affiliation(s)
- Kinga K Nagy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., 1117, Budapest, Hungary
| | - Kristóf Takács
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Imre Németh
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary
| | - Bálint Varga
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Eötvös Loránd University, 1117, Budapest, Hungary
- Uratim Ltd., 1118, Budapest, Hungary
| | - Mónika Molnár
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary.
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem Rkp. 3., 1111, Budapest, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., 1117, Budapest, Hungary.
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Tang L, Sun Y, Lu W, Chen X, Mosa A, Minkina T, Gao Y, Ling W. A novel remediation strategy of mixed calcium peroxide and degrading bacteria for polycyclic aromatic hydrocarbon contaminated water. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134122. [PMID: 38552397 DOI: 10.1016/j.jhazmat.2024.134122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of toxic organic pollutants commonly detected in the aqueous phase. Traditional biodegradation is inefficient and advanced oxidation technologies are expensive. In the current study, a novel strategy was developed using calcium peroxide (CP) and PAH-degrading bacteria (PDB) to effectively augment PAH degradation by 28.62-59.22%. The PDB consisted of the genera Acinetobacter, Stenotrophomonas, and Comamonas. Applying the response surface model (RSM), the most appropriate parameters were identified, and the predictive degradation rates of phenanthrene (Phe), pyrene (Pyr), and ΣPAHs were 98%, 76%, and 84%, respectively. The constructed mixed system could reduce 90% of Phe and more than 60% of ΣPAHs and will perform better at pH 5-7 and lower salinity. Because PAHs tend to bind to dissolved organic matter (DOM) with larger molecular weights, humic acid (HA) had a larger negative effect on the PAH-degradation efficiency of the CP-PDB mixed system than fulvic acid (FA). The proposed PAH-degradation pathways in the mixed system were based on the detection of intermediates at different times. The investigation constructed and optimized a novel environmental PAH-degradation strategy. The synergistic application of PDB and oxidation was extended for organic contaminant degradation in aqueous environments.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yulong Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyi Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuwen Chen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Tatiana Minkina
- Academy of Biology and Biotechnology named after D I Ivanovsky, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Tang L, Yan J, Zhou X, Wang J, Gao Y, Mosa A, Czech B, Oleszczuk P, Ling W. Dissolved organic matter influences the indigenous bacterial community and polycyclic aromatic hydrocarbons biodegradation in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171662. [PMID: 38485009 DOI: 10.1016/j.scitotenv.2024.171662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
In polycyclic aromatic hydrocarbon (PAH) contaminated soils, bioremediation is superior to other strategies owing to its low cost and environmental friendliness. However, dissolved organic matter (DOM) and indigenous bacterial communities can affect the efficiency of PAH-degrading bacteria (PDB). This study found that exogenous PDB (C1) including the genera Acinetobacter, Stenotrophomonas, and Comamonas, decreased the bacterial diversity of Alfisol, Ultisol, Inceptisol, and Mollisol, and DOM enhanced the diffusion of PDB and the bioavailability of PAH. In addition, bacteria preferred to ingest low molecular weight DOM fractions, and the abundances of lipid-like and protein-like substances decreased by 0.12-3.03 % and 1.73-4.60 %. The DOM fractions had a more marked influence on the indigenous bacteria than the exogenous PDB, and PDB dominated the PAH biodegradation process in the soils. More COO functional groups promoted the utilization of higher molecular weight-related homologue fractions by bacteria, and lower molecular weight fractions carrying more CH2 functional groups declined during biodegradation. This study investigated the variations in bacterial communities during biodegradation and revealed the effects of DOM fractions on biodegradation in PAH-contaminated soils at the molecular level. These results will promote the development of bioremediation strategies for organics-contaminated soil and provide guidance for prediction models of soil biodegradation kinetics.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayi Yan
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xian Zhou
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt
| | - Bozena Czech
- Department of Radiochemistry and Environmental Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland
| | - Patryk Oleszczuk
- Department of Radiochemistry and Environmental Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Tang L, Bao Z, Zhao X, Wang X, Gao Y, Lu C, Ling W. Variations of different PAH fractions and bacterial communities during the biological self-purification in the soil vertical profile. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131903. [PMID: 37352779 DOI: 10.1016/j.jhazmat.2023.131903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/29/2023] [Accepted: 06/18/2023] [Indexed: 06/25/2023]
Abstract
Wild PAH-contaminated sites struggle to provide continuous and stable monitoring, resulting in the potential risks of contaminated soil utilization could not be evaluated effectively. This work provided a 9-months laboratory simulation which was close to the natural ecological process. These results believed that PAH-degrading bacteria (PDB) preferred to degrade organic extracted PAH (PAH_OS) and fresh bound-PAH (79.36-99.97%). The formation and migration efficiency of PAH binding with HA humic acid (HA) (PAH_HA) was lower than that of PAH binding with fulvic acid (FA) and humin (HM) (PAH_FA and PAH_HM), leading to PAH_HA had more persistent retention and influenced bacterial communities in shallow soils. Besides, phylum Proteobacteria gradually dominated the bacterial community and decreased 12.05-20.48% diversity at all depths during the biological self-purification process. Although the effect of this process enhanced the abundance of 28 genes 16 s rRNA and three PAH-degrading genes (PDGs) by 5.91-2047.34 times (phe, nahAc and nidA), the top 30 genera maintained their ecological characteristics. This study provided insights into the important influencing factor and mechanism of the biological self-purification processes and discerned the linkages between bacterial communities and environmental variables in the vertical profile, which is important to the isolation and application of PDB and ecological risk assessment.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongkang Bao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuqiang Zhao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinbo Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Lu
- National Agricultural Experiment Station for Agricultural Environment, Luhe, Ministry of Agriculture, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Tang L, Zhao X, Chen X, Jiang Y, Gudda F, Wang Y, Ling W. Distribution of bound-PAH residues and their correlations with the bacterial community at different depths of soil from an abandoned chemical plant site. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131328. [PMID: 37043862 DOI: 10.1016/j.jhazmat.2023.131328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
The situ pollutant residue and microbial characteristics in contaminated environments are crucial for ecological restoration and soil utilization. This work reported the variation of polycyclic aromatic hydrocarbon (PAH) residues and the bacterial community at different depths in an aged-abandoned site. These results unveiled that over 90% of low molecular weight (LMW) and medium molecular weight (MMW), 52.84-76.88% of high molecular weight (HMW) bound-PAH (BP) residues were sequestrated in humin (HM). The stresses of PAH and soil depth enhanced the frequency of bacteria associations, especially positive associations. We enriched and cultured PAH degradation bacteria (PDB) from the sampling site mainly consisting of Pseudomonas and Acinetobacter, which were originally 0.39-0.52% abundant in the sampling site. The abundances of PDB and PAH-degradation genes (PDGs) were higher at shallower depths and increased with high PAH concentration. Simultaneously, Pearson correlation analysis and experimental verification found that the process of PAH binding with SOM limited the further increase of PDB and PDGs in PAH-contaminated sites. These findings may illustrate possible ecological risks of contaminated soils and provide guidance for the isolation and application of PDB.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuqiang Zhao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuwen Chen
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Jiang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fredrick Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhao Wang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Tu Y, Shen J, Peng Z, Xu Y, Li Z, Liang J, Wei Q, Zhao H, Huang J. Biochar-Dual Oxidant Composite Particles Alleviate the Oxidative Stress of Phenolic Acid on Tomato Seed Germination. Antioxidants (Basel) 2023; 12:antiox12040910. [PMID: 37107285 PMCID: PMC10136075 DOI: 10.3390/antiox12040910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Phenolic acid is a well-known allelochemical, but also a pollutant in soil and water impeding crop production. Biochar is a multifunctional material widely used to mitigate the phenolic acids allelopathic effect. However, phenolic acid absorbed by biochar can still be released. In order to improve the removal efficiency of phenolic acids by biochar, the biochar-dual oxidant (BDO) composite particles were synthesized in this study, and the underlying mechanism of the BDO particles in ameliorating p-coumaric acid (p-CA) oxidative damage to tomato seed germination was revealed. Upon p-CA treatment, the BDO composite particles application increased the radical length, radical surface area, and germination index by 95.0%, 52.8%, and 114.6%, respectively. Compared to using biochar or oxidants alone, the BDO particles addition resulted in a higher removal rate of p-CA and produced more O2•-, HO•, SO4•- and 1O2 radicals via autocatalytic action, suggesting that BDO particles removed phenolic acid by both adsorption and free radical oxidation. The addition of BDO particles maintained the levels of the antioxidant enzyme activity close to the control, and reduced the malondialdehyde and H2O2 by 49.7% and 49.5%, compared to the p-CA treatment. Integrative metabolomic and transcriptomic analyses revealed that 14 key metabolites and 62 genes were involved in phenylalanine and linoleic acid metabolism, which increased dramatically under p-CA stress but down-regulated with the addition of BDO particles. This study proved that the use of BDO composite particles could alleviate the oxidative stress of phenolic acid on tomato seeds. The findings will provide unprecedented insights into the application and mechanism of such composite particles as continuous cropping soil conditioners.
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Affiliation(s)
- Yuting Tu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jinchun Shen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zhiping Peng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou 510640, China
| | - Yanggui Xu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou 510640, China
| | - Zhuxian Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jianyi Liang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qiufang Wei
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hongbo Zhao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jichuan Huang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Guangzhou 510640, China
- Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Guangzhou 510640, China
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Tang L, Gudda FO, Wu C, Ling W, El-Ramady H, Mosa A, Wang J. Contributions of partition and adsorption to polycyclic aromatic hydrocarbons sorption by fractionated soil at different particle sizes. CHEMOSPHERE 2022; 301:134715. [PMID: 35487352 DOI: 10.1016/j.chemosphere.2022.134715] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Partition and adsorption of polycyclic aromatic hydrocarbons (PAHs) are critical mechanisms determining their fate at the solid-liquid interface. The complexity of soil composition makes it difficult to distinguish between partition and adsorption, and bates the accuracy of the research results. This study found that the composition and structure of the soil particles (SAs) of varying particle sizes were significantly different. Partition contributed significantly to phenanthrene (Phe) sorption in SAs over 0.002 mm. However, PAHs had the highest sorption coefficient (Kd) in SA less than 0.002 mm (SA-3), and the lower aqueous phase equilibrium concentration of Phe, the greater the adsorption effect. According to morphology and structural analysis, Fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS), interactions of micropores, soil organic matter (SOM) and minerals enhanced the sorption of PAHs. Additionally, thermogravimetry and mass spectrometry (TG-MS) results proved that SOM could inhibit the release of PAHs adsorbed in SAs during heating process. We observed that the Log Koc of PAHs was the most important factor in determining the Kd in SAs applying principal component analyses (PCA), and they have significant linear relationships (R2 = 0.79-0.93). These findings provide new understandings on interface reactivity of PAHs sorption to soils and the development of interface model.
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Affiliation(s)
- Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chenxi Wu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hassan El-Ramady
- Soil and Water Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516, Mansoura, Egypt
| | - Jian Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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