1
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Ningthoujam R, Pinyakong O. Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134557. [PMID: 38735188 DOI: 10.1016/j.jhazmat.2024.134557] [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: 02/25/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]
Abstract
Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.
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Affiliation(s)
- Ritu Ningthoujam
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Onruthai Pinyakong
- Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT), Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand.
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2
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Kushwaha M, Singh D, Akhter Y, Chatterjee S. Biodegradation of DEP, DIBP, and BBP by a psychrotolerant Sphingobium yanoikuyae strain P4: Degradation potentiality and mechanism study. Arch Microbiol 2024; 206:254. [PMID: 38727835 DOI: 10.1007/s00203-024-03977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/19/2024] [Accepted: 04/24/2024] [Indexed: 06/18/2024]
Abstract
Phthalic acid esters (PAEs) are human made chemicals widely used as plasticizers to enhance the flexibility of plastic products. Due to the lack of chemical bonding between phthalates and plastics, these materials can easily enter the environment. Deleterious effects caused by this chemo-pollutant have drawn the attention of the scientific community to remediate them from different ecosystem. In this context, many bacterial strains have been reported across different habitats and Sphingobium yanoikuyae strain P4 is among the few psychrotolerant bacterial species reported to biodegrade simple and complex phthalates. In the present study, biodegradation of three structurally different PAEs viz., diethyl phthalate (DEP), di-isobutyl phthalate (DIBP), and butyl benzyl phthalate (BBP) have been investigated by the strain P4. Quantitative analyses through High-performance liquid chromatography (HPLC) revealed that the bacterium completely degraded 1 g/L of DEP, DIBP, and BBP supplemented individually in minimal media pH 7.0 within 72, 54, and 120 h of incubation, respectively, at 28 °C and under shake culture condition (180 rpm). In addition, the strain could grow in minimal media supplemented individually with up to 3 g/L of DEP and 10.0 g/L of DIBP and BBP at 28 °C and pH 7.0. The strain also could grow in metabolites resulting from biodegradation of DEP, DIBP, and BBP, viz. n-butanol, isobutanol, butyric acid, ethanol, benzyl alcohol, benzoic acid, phthalic acid, and protocatechuic acid. Furthermore, phthalic acid and protocatechuic acid were also detected as degradation pathway metabolites of DEP and DIBP by HPLC, which gave an initial idea about the biodegradation pathway(s) of these phthalates.
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Affiliation(s)
- Madhulika Kushwaha
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, District-Kangra, Himachal Pradesh, 176206, India
| | - Dharam Singh
- Molecular and Microbial Genetics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, District-Kangra, Himachal Pradesh, 176061, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, District-Kangra, Himachal Pradesh, 176206, India.
- Bioremediation and Metabolomics Research Group, Department of Ecology & Environmental Sciences, School of Life Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605 014, India.
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3
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Sun Y, Zhang Y, Ma Y, Xin R, Li X, Niu Z. 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. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123146. [PMID: 38101529 DOI: 10.1016/j.envpol.2023.123146] [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: 09/07/2023] [Revised: 11/18/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
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.
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Affiliation(s)
- Yueling Sun
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ying Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yongzheng Ma
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Rui Xin
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaofeng Li
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiguang Niu
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China; International Joint Institute of Tianjin University, Fuzhou, Fuzhou, 350205, China.
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Rashmi M, Singh T, Rajput NS, Kulshreshtha S. Biodegradation of di-2-ethylhexyl phthalate by Bacillus firmus MP04 strain: parametric optimization using full factorial design. Biodegradation 2023; 34:567-579. [PMID: 37354272 DOI: 10.1007/s10532-023-10043-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Di-2-ethylhexyl phthalate (DEHP) is used as a plasticizer in making plastics and released from landfills. This study attempted to degrade DEHP using microbial isolates. Isolates of Bacillus spp. were tested for their efficacy in degrading DEHP. Degradation was assessed using liquid chromatography-mass spectrometry (LC-MS). The most efficient DEHP degradation was achieved by Bacillus firmus MP04, which has been identified as Bacillus firmus MP04. This strain was found to use DEHP as the sole source of carbon without carbon source supplementation. Full factorial design was used to optimize the conditions for DEHP degradation which revealed the suitability of pH 7, 5% salt concentration, 20 to 37 °C temperature, and yeast extract as a nitrogen source. LC-MS elucidated the possible degradation mechanism via benzoic acid formation. However, prolonged incubation formed a typical compound denatonium benzoate due to reactions with other compounds. As maximum degradation was achieved in 4 days, prolonged incubation is not suggested. It can be concluded that new strain Bacillus firmus MP04 is the most efficient strain among all the tested strains for DEHP degradation.
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Affiliation(s)
- Madhavi Rashmi
- Department of Biotechnology, Magadh University, Bodh Gaya, Bihar, India
| | - Tanuja Singh
- Department of Botany, Patliputra University, Patna, Bihar, India
| | - Nitesh Singh Rajput
- Amity School of Engineering and Technology, Amity University Rajasthan, Jaipur, Rajasthan, 303007, India
| | - Shweta Kulshreshtha
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, 303007, India.
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Puranik S, Shukla L, Kundu A, Kamil D, Paul S, Venkadasamy G, Salim R, Singh SK, Kumar D, Kumar A. Exploring Potent Fungal Isolates from Sanitary Landfill Soil for In Vitro Degradation of Dibutyl Phthalate. J Fungi (Basel) 2023; 9:jof9010125. [PMID: 36675946 PMCID: PMC9860837 DOI: 10.3390/jof9010125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
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.
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Affiliation(s)
- Shriniketan Puranik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Livleen Shukla
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Correspondence: (L.S.); (A.K.); Tel.: +91-880-093-3066 (L.S.); +91-896-063-9724 (A.K.)
| | - Aditi Kundu
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sangeeta Paul
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Govindasamy Venkadasamy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajna Salim
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sandeep Kumar Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
- Correspondence: (L.S.); (A.K.); Tel.: +91-880-093-3066 (L.S.); +91-896-063-9724 (A.K.)
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6
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Efficient biodegradation of di-(2-ethylhexyl) phthalate by a novel strain Nocardia asteroides LMB-7 isolated from electronic waste soil. Sci Rep 2022; 12:15262. [PMID: 36088485 PMCID: PMC9464244 DOI: 10.1038/s41598-022-19752-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/02/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe di-2-ethylhexyl phthalate (DEHP) degrading strain LMB-7 was isolated from electronic waste soil. According to its biophysical/biochemical characteristics and 16S rRNA gene analysis, the strain was identified as Nocardia asteroides. Optimal pH and temperature for DEHP degradation were 8.0 and 30 °C, respectively, and DEHP removal reached 97.11% after cultivation for 24 h at an initial concentration of 400 mg/L. As degradation intermediates, di-butyl phthalates, mono-2-ethylhexyl phthalate and 2-ethylhexanol could be identified, and it could be confirmed that DEHP was completely degraded by strain LMB-7. To our knowledge, this is a new report of DEHP degradation by a strain of Nocardia asteroides, at rates higher than those reported to date. This finding provides a new way for DEHP elimination from environment.
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7
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Wu M, Tang J, Zhou X, Lei D, Zeng C, Ye H, Cai T, Zhang Q. Isolation of Dibutyl Phthalate-Degrading Bacteria and Its Coculture with Citrobacter freundii CD-9 to Degrade Fenvalerate. J Microbiol Biotechnol 2022; 32:176-186. [PMID: 35058397 PMCID: PMC9628840 DOI: 10.4014/jmb.2110.10048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Continued fenvalerate use has caused serious environmental pollution and requires large-scale remediation. Dibutyl phthalate (DBP) was discovered in fenvalerate metabolites degraded by Citrobacter freundii CD-9. Coculturing is an effective method for bioremediation, but few studies have analyzed the degradation pathways and potential mechanisms of cocultures. Here, a DBP-degrading strain (BDBP 071) was isolated from soil contaminated with pyrethroid pesticides (PPs) and identified as Stenotrophomonas acidaminiphila. The optimum conditions for DBP degradation were determined by response surface methodology (RSM) analysis to be 30.9 mg/l DBP concentration, pH 7.5, at a culture temperature of 37.2°C. Under the optimized conditions, approximately 88% of DBP was degraded within 48 h and five metabolites were detected. Coculturing C. freundii CD-9 and S. acidaminiphila BDBP 071 promoted fenvalerate degradation. When CD-9 was cultured for 16 h before adding BDBP 071, the strain inoculation ratio was 5:5 (v/v), fenvalerate concentration was 75.0 mg/l, fenvalerate was degraded to 84.37 ± 1.25%, and DBP level was reduced by 5.21 mg/l. In addition, 12 fenvalerate metabolites were identified and a pathway for fenvalerate degradation by the cocultured strains was proposed. These results provide theoretical data for further exploration of the mechanisms used by this coculture system to degrade fenvalerate and DBP, and also offer a promising method for effective bioremediation of PPs and their related metabolites in polluted environments.
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Affiliation(s)
- Min Wu
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Jie Tang
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China,Corresponding authors J. Tang Phone: +86-28-87720552 Fax: +86-28-87720552 E-mail:
| | - Xuerui Zhou
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Dan Lei
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Chaoyi Zeng
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Hong Ye
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Ting Cai
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China
| | - Qing Zhang
- Key Laboratory of Food Biotechnology, College of Food and Bioengineering, Xihua University, Chengdu 610039, Sichuan, P.R. China,
Q. Zhang E-mail:
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8
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Zhao Z, Liu C, Xu Q, Ahmad S, Zhang H, Pang Y, Aikemu A, Liu Y, Yan H. Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y. World J Microbiol Biotechnol 2021; 37:212. [PMID: 34738191 DOI: 10.1007/s11274-021-03181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022]
Abstract
A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.
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Affiliation(s)
- Zhenzhen Zhao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Shahbaz Ahmad
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Haiyang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yu Pang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Abudumukeyiti Aikemu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Carmen S. Microbial capability for the degradation of chemical additives present in petroleum-based plastic products: A review on current status and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123534. [PMID: 33254737 DOI: 10.1016/j.jhazmat.2020.123534] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 06/12/2023]
Abstract
Plastic additives are present as pollutants in the environment because they are released from plastics and have been reported to be toxic to mammals. Due to this toxicity, it is crucial to develop ecofriendly tools to decontaminate the environment. Microorganisms are a promising alternative for efficient and effective plastic additive removal. This review describes the current knowledge and significant advances in the microbial degradation of plastic additives (i.e. plasticizers, flame retardants, stabilizers and antioxidants) and biotechnological research strategies that are being used to accelerate the biodegradation process of these additives. It is expected that further research supported by advances in genomics, proteomics, gene expression, enzyme immobilization, protein design, and nanotechnology can substantially increase our knowledge to enhance the enzymatic degradation efficiency, which will accelerate plastic additive degradation and establish successful and cost-effective bioremediation processes. Investigations should also address the identification of the enzymes involved in the degradation process and their catalytic mechanisms to achieve full metabolization of organopollutants (i.e. plastic additives) while avoiding harmful plastic additive biodegradation products. Microorganisms and their enzymes undoubtedly represent a potential resource for developing promising environmental biotechnologies, as they have the best systems for pollutant degradation, and their actions are essential for decontaminating the environment.
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Affiliation(s)
- Sánchez Carmen
- Laboratory of Biotechnology, Research Centre for Biological Sciences, Universidad Autónoma de Tlaxcala, Ixtacuixtla, C.P.90120, Tlaxcala, Mexico.
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10
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Liu T, Li J, Qiu L, Zhang F, Linhardt RJ, Zhong W. Combined genomic and transcriptomic analysis of the dibutyl phthalate metabolic pathway in
Arthrobacter
sp. ZJUTW. Biotechnol Bioeng 2020; 117:3712-3726. [DOI: 10.1002/bit.27524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Tengfei Liu
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Jun Li
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Lequan Qiu
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy New York
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Troy New York
| | - Weihong Zhong
- College of Biotechnology and Bioengineering Zhejiang University of Technology Hangzhou China
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11
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Li X, Wang J, Jia Y, Reheman A, Yan Y. The Genome Analysis of Methylobacterium populi YC-XJ1 with Diverse Xenobiotics Biodegrading Capacity and Degradation Characteristics of Related Hydrolase. Int J Mol Sci 2020; 21:ijms21124436. [PMID: 32580446 PMCID: PMC7352507 DOI: 10.3390/ijms21124436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Methylobacterium populi YC-XJ1 isolated from desert soil exhibited a diverse degrading ability towards aromatic oxyphenoxypropionic acid esters (AOPPs) herbicide, phthalate esters (PAEs), organophosphorus flame retardants (OPFRs), chlorpyrifos and phoxim. The genome of YC-XJ1 was sequenced and analyzed systematically. YC-XJ1 contained a large number of exogenous compounds degradation pathways and hydrolase resources. The quizalofop-p-ethyl (QPE) degrading gene qpeh2 and diethyl phthalate (DEP) degrading gene deph1 were cloned and expressed. The characteristics of corresponding hydrolases were investigated. The specific activity of recombinant QPEH2 was 0.1 ± 0.02 U mg-1 for QPE with kcat/Km values of 1.8 ± 0.016 (mM-1·s-1). The specific activity of recombinant DEPH1 was 0.1 ± 0.02 U mg-1 for DEP with kcat/Km values of 0.8 ± 0.02 (mM-1·s-1). This work systematically illuminated the metabolic versatility of strain YC-XJ1 via the combination of genomics analysis and laboratory experiments. These results suggested that strain YC-XJ1 with diverse xenobiotics biodegrading capacity was a promising candidate for the bioremediation of polluted sites.
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Affiliation(s)
- Xianjun Li
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Junhuan Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Yang Jia
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Aikebaier Reheman
- Key Laboratory of Toxicology, Ningde Normal University, Ningde 352100, China
- Correspondence: (A.R.); (Y.Y.); Tel.: +86-10-82109685 (Y.Y.)
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
- Correspondence: (A.R.); (Y.Y.); Tel.: +86-10-82109685 (Y.Y.)
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12
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Zhang L, Hu Q, Liu B, Li F, Jiang JD. Characterization of a Linuron-Specific Amidohydrolase from the Newly Isolated Bacterium Sphingobium sp. Strain SMB. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4335-4345. [PMID: 32207940 DOI: 10.1021/acs.jafc.0c00597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The phenylurea herbicide linuron is globally used and has caused considerable concern because it leads to environmental pollution. In this study, a highly efficient linuron-transforming strain Sphingobium sp. SMB was isolated, and a gene (lahB) responsible for the hydrolysis of linuron to 3,4-dichloroaniline and N,O-dimethylhydroxylamine was cloned from the genome of strain SMB. The lahB gene encodes an amidohydrolase, which shares 20-53% identity with other biochemically characterized amidohydrolases, except for the newly reported linuron hydrolase Phh (75%). The optimal conditions for the hydrolysis of linuron by LahB were determined to be pH 7.0 and 30 °C, and the Km value of LahB for linuron was 37.3 ± 1.2 μM. Although LahB and Phh shared relatively high identity, LahB exhibited a narrow substrate spectrum (specific for linuron) compared to Phh (active for linuron, diuron, chlortoluron, etc.). Sequence analysis and site-directed mutagenesis revealed that Ala261 of Phh was the key amino acid residue affecting the substrate specificity. Our study provides a new amidohydrolase for the specific hydrolysis of linuron.
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Bin Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Feng Li
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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13
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Wright RJ, Bosch R, Gibson MI, Christie-Oleza JA. Plasticizer Degradation by Marine Bacterial Isolates: A Proteogenomic and Metabolomic Characterization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2244-2256. [PMID: 31894974 PMCID: PMC7031849 DOI: 10.1021/acs.est.9b05228] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 05/19/2023]
Abstract
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.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- School for Resource and Environmental Studies, Dalhousie University, Halifax B3H 4R2, Canada
- E-mail: (R.J.W.)
| | - Rafael Bosch
- University of the Balearic Islands, Palma 07122, Spain
- IMEDEA (CSIC-UIB), Esporles 07190, Spain
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Medical School, University
of Warwick, Coventry CV4 7AL, U.K.
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- University of the Balearic Islands, Palma 07122, Spain
- IMEDEA (CSIC-UIB), Esporles 07190, Spain
- E-mail: (J.A.C.-O.)
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14
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Sun R, Wang L, Jiao Y, Zhang Y, Zhang X, Wu P, Chen Z, Feng C, Li Y, Li X, Yan L. Metabolic process of di-n-butyl phthalate (DBP) by Enterobacter sp. DNB-S2, isolated from Mollisol region in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113344. [PMID: 31668953 DOI: 10.1016/j.envpol.2019.113344] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Ruixue Sun
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Lei Wang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yaqi Jiao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Xing Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Pan Wu
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, People's Republic of China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, People's Republic of China
| | - Chengcheng Feng
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Ying Li
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiaoqian Li
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Lilong Yan
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, People's Republic of China
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