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Zhai Q, Zheng S, Zhang C, Lu Z, Liang S, Li R, Zhang X, Pan H, Zhang H. Kj-mhpC Enzyme in Klebsiella jilinsis 2N3 Is Involved in the Degradation of Chlorimuron-Ethyl via De-Esterification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5176-5184. [PMID: 38417018 DOI: 10.1021/acs.jafc.3c08918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Microbial degradation is a highly efficient and reliable approach for mitigating the contamination of sulfonylurea herbicides, such as chlorimuron-ethyl, in soil and water. In this study, we aimed to assess whether Kj-mhpC plays a pivotal role in the degradation of chlorimuron-ethyl. Kj-mhpC enzyme purified via prokaryotic expression exhibited the highest catalytic activity for chlorimuron-ethyl at 35 °C and pH 7. Bioinformatic analysis and three-dimensional homologous modeling of Kj-mhpC were conducted. Additionally, the presence of Mg+ and Cu2+ ions partially inhibited but Pb2+ ions completely inhibited the enzymatic activity of Kj-mhpC. LC/MS revealed that Kj-mhpC hydrolyzes the ester bond of chlorimuron-ethyl, resulting in the formation of 2-(4-chloro-6-methoxypyrimidine-2-amidoformamidesulfonyl) benzoic acid. Furthermore, the point mutation of serine at position 67 (Ser67) confirmed that it is the key amino acid at the active site for degrading chlorimuron-ethyl. This study enhanced the understanding of how chlorimuron-ethyl is degraded by microorganisms and provided a reference for bioremediation of the environment polluted with chlorimuron-ethyl.
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Affiliation(s)
- Qianhang Zhai
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shuanglan Zheng
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zhou Lu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shuang Liang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Ranhong Li
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xianghui Zhang
- College of Plant Science, Jilin University, Changchun 130118, China
| | - Hongyu Pan
- College of Plant Science, Jilin University, Changchun 130118, China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
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Jannat MAH, Park SH, Hwang S. Modeling interactions of Clostridium cadaveris and Clostridium sporogenes in anaerobic acidogenesis of glucose and peptone. BIORESOURCE TECHNOLOGY 2024; 393:130099. [PMID: 38013037 DOI: 10.1016/j.biortech.2023.130099] [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: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
This study focuses on developing a mathematical model to assess interaction among acidogenic bacteria during the anaerobic degradation of two substrates. Clostridium cadaveris and Clostridium sporogenes were cultured in various combinations with glucose and peptone. Parameter estimates are given for both conventional Monod parameters from single substrate-single species cultures and sum kinetics with interaction parameters obtained from dual substrate-single species cultures. The presence of multiple substrates led to both inhibitory and enhancing effects on biodegradation rates for dual substrates compared to single substrate cultures. A new model of interspecies interaction was developed within the framework of Lotka-Volterra incorporating substrate interaction parameters, with a focus on accuracy, realism, simplicity, and biological significance. The model demonstrated competitive interaction for resource sharing and the additional non-linearity parameter eliminated the constraint of the linear relationship between growth rate and population density.
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Affiliation(s)
- Md Abu Hanifa Jannat
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
| | - Sang Hyeok Park
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea; Yonsei University Institute for Convergence Research and Education in Advanced Technology (I-CREATE), 85, Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea.
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Miao L, Sun S, Ma T, Abdelrahman Yousif Abdellah Y, Wang Y, Mi Y, Yan H, Sun G, Hou N, Zhao X, Li C, Zang H. A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6. Appl Environ Microbiol 2023; 89:e0148922. [PMID: 36847539 PMCID: PMC10057884 DOI: 10.1128/aem.01489-22] [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: 08/31/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.
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Affiliation(s)
- Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Tian Ma
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | | | - Yue Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Yaozu Mi
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Haohao Yan
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
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Zhang Y, Geng Y, Li S, Shi T, Ma X, Hua R, Fang L. Efficient Knocking Out of the Organophosphorus Insecticides Degradation Gene opdB in Cupriavidus nantongensis X1 T via CRISPR/ Cas9 with Red System. Int J Mol Sci 2023; 24:ijms24066003. [PMID: 36983076 PMCID: PMC10056268 DOI: 10.3390/ijms24066003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Cupriavidus nantongensis X1T is a type strain of the genus Cupriavidus, that can degrade eight kinds of organophosphorus insecticides (OPs). Conventional genetic manipulations in Cupriavidus species are time-consuming, difficult, and hard to control. The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) system has emerged as a powerful tool for genome editing applied in prokaryotes and eukaryotes due to its simplicity, efficiency, and accuracy. Here, we combined CRISPR/Cas9 with the Red system to perform seamless genetic manipulation in the X1T strain. Two plasmids, pACasN and pDCRH were constructed. The pACasN plasmid contained Cas9 nuclease and Red recombinase, and the pDCRH plasmid contained the dual single-guide RNA (sgRNA) of organophosphorus hydrolase (OpdB) in the X1T strain. For gene editing, two plasmids were transferred to the X1T strain and a mutant strain in which genetic recombination had taken place, resulting in the targeted deletion of opdB. The incidence of homologous recombination was over 30%. Biodegradation experiments suggested that the opdB gene was responsible for the catabolism of organophosphorus insecticides. This study was the first to use the CRISPR/Cas9 system for gene targeting in the genus Cupriavidus, and it furthered our understanding of the process of degradation of organophosphorus insecticides in the X1T strain.
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Affiliation(s)
- Yufei Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shengyang Li
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xin Ma
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
| | - Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
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Yu Z, Gu W, Yang Y, Li X, Li X, Li T, Wang J, Su Z, Li X, Dai Y, Xu M, Zhang H. Whole-Genome Sequencing of a Chlorimuron-Ethyl-Degrading Strain: Chenggangzhangella methanolivorans CHL1 and Its Degrading Enzymes. Microbiol Spectr 2022; 10:e0182222. [PMID: 35861510 PMCID: PMC9430300 DOI: 10.1128/spectrum.01822-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, and its long-term residues cause serious environmental problems. Biodegradation of chlorimuron-ethyl is effective and feasible, and many degrading strains have been obtained, but still, the genes and enzymes involved in this degradation are often unclear. In this study, whole-genome sequencing was performed on chlorimuron-ethyl-degrading strain, Chenggangzhangella methanolivorans CHL1. The complete genome of strain CHL1 contains one circular chromosome of 5,542,510 bp and a G+C content of 68.17 mol%. Three genes, sulE, pnbA, and gst, were predicted to be involved in the degradation of chlorimuron-ethyl, and this was confirmed by gene knockout and gene complementation experiments. The three genes were cloned and expressed in Escherichia coli BL21 (DE3) to allow for the evaluation of the catalytic activities of the respective enzymes. The glutathione-S-transferase (GST) catalyzes the cleavage of the sulfonylurea bridge of chlorimuron-ethyl, and the esterases, PnbA and SulE, both de-esterify it. This study identifies three key functional genes of strain CHL1 that are involved in the degradation of chlorimuron-ethyl and also provides new approaches by which to construct engineered bacteria for the bioremediation of environments polluted with sulfonylurea herbicides. IMPORTANCE Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, worldwide. However, its residues in soil and water have a potent toxicity toward sensitive crops and other organisms, such as microbes and aquatic algae, and this causes serious problems for the environment. Microbial degradation has been demonstrated to be a feasible and promising strategy by which to eliminate xenobiotics from the environment. Many chlorimuron-ethyl-degrading microorganisms have been reported, but few studies have investigated the genes and enzymes that are involved in the degradation. In this work, two esterase-encoding genes (sulE, pnbA) and a glutathione-S-transferase-encoding gene (gst) responsible for the detoxification of chlorimuron-ethyl by strain Chenggangzhangella methanolivorans CHL1 were identified, then cloned and expressed in Escherichia coli BL21 (DE3). These key chlorimuron-ethyl-degrading enzymes are candidates for the construction of engineered bacteria to degrade this pesticide and enrich the resources for bioremediating environments polluted with sulfonylurea herbicides.
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Affiliation(s)
- Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang, China
| | - Jian Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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6
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Zhu C, Huang H, Chen Y. Recent advances in biological removal of nitroaromatics from wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119570. [PMID: 35667518 DOI: 10.1016/j.envpol.2022.119570] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Various nitroaromatic compounds (NACs) released into the environment cause potential threats to humans and animals. Biological treatment is valued for cost-effectiveness, environmental friendliness, and availability when treating wastewater containing NACs. Considering the significance and wide use of NACs, this review focuses on recent advances in biological treatment systems for NACs removal from wastewater. Meanwhile, factors affecting biodegradation and methods to enhance removal efficiency of NACs are discussed. The selection of biological treatment system needs to consider NACs loading and cost, and its performance is affected by configuration and operation strategy. Generally, sequential anaerobic-aerobic biological treatment systems perform better in mineralizing NACs and removing co-pollutants. Future research on mechanism exploration of NACs biotransformation and performance optimization will facilitate the large-scale application of biological treatment systems.
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Affiliation(s)
- Cuicui Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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Lu H, Zhou Y, Fu Z, Wang X, Zhou J, Guo W. Mutual interaction between the secreted flavins and immobilized quinone in anaerobic removal of high-polarity aromatic compounds containing nitrogen by Shewanella sp. RQs-106. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128595. [PMID: 35247734 DOI: 10.1016/j.jhazmat.2022.128595] [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: 09/17/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
The immobilized anthraquinone-2-sulfonate (iAQS) could significantly promote anaerobic biotransformation of the contaminants. During this process, the role of flavins secreted by bacteria remains unclear. In the present study, mutual interaction between extracellular flavins and AQS-modified polyurethane foam (AQS-PUF) during the reduction of azo dye Acid Red 18 and 3-nitrobenzenesulfonate (3-NBS) was investigated. Results showed that the amount of extracellular flavins secreted by Shewanella sp. RQs-106 was positively correlated with the concentration of iAQS ranging from 10 to 100 μM. The presence of iAQS resulted in the increased concentration of extracellular and intracellular flavins, implying that iAQS could induce the synthesis and secretion of flavins. The deletion of gene bfe encoding the flavin adenine dinucleotide exporter resulted in approximately 63.8% decrease in the amount of extracellular flavins. Further analysis showed that the decreased amount of extracellular flavins could contribute to around 50.8% reduction of iAQS. Moreover, around 23.2% and 34.0% decreases were observed in AQS-PUF-mediated removal rates of AR 18 and 3-NBS by mutant lacking bfe gene, respectively, compared with that by wild type strain RQs-106. These results indicated that the secreted flavins played an important role in the bio-reduction of AQS-PUF, resulting in their contribution to AQS-PUF-mediated removals of high-polarity aromatic compounds containing nitrogen.
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Affiliation(s)
- Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yang Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ze Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaolei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Wanqian Guo
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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Min J, Fang S, Peng J, Lv X, Xu L, Li Y, Hu X. Microbial detoxification of 2,4,6-tribromophenol via a novel process with consecutive oxidative and hydrolytic debromination: Biochemical, genetic and evolutionary characterization. ENVIRONMENTAL RESEARCH 2022; 205:112494. [PMID: 34890595 DOI: 10.1016/j.envres.2021.112494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
As a typical brominated flame retardants (BFRs), 2,4,6-tribromophenol (TBP) has serious hazard to the environmental health and its environmental fate has attracted considerable attention. Dehalogenation reaction plays key role in microbial TBP degradation and detoxification. So far, several halophenols-degrading enzymes have been reported to transform their substrate by oxidative dehalogenation; however, the molecular and biochemistry characterization of microbial hydrolytic dehalogenation is limited. In this study, Cupriavidus sp. CNP-8 with high TBP degradation activity was found to degrade TBP via an obviously differnet pathway as compared to other reported TBP-degraders. The transcription of hnp genes were significantly upregulated with TBP stimulation, indicating their involvment in TBP degradation. Enzymatic assays with 18O-labeling experiments showed that HnpAB, a two-component FAD-dependent monooxygenase, transformed TBP via consecutive oxidative and hydrolytic debromination reactions with the formation of 6-bromo-1,2,4-benzenetriol (BBT) as the ring-cleavage substrate. The function of the BBT ring-cleavage enzyme (HnpC) was also characterized both in vitro and in vivo. This finding provides new molecular mechanism of microbial detoxification of TBP and novel information of the environmental fate of this BFRs. Furthermore, to investigate the frequency of this novel dehalogenation mechanism in microbes, we also analyzed the distribution as well as the genetic structure of the hnpABC cluster by comparative genomics. Although hnpA homolog is distributed in several bacterial genera including Cupriavidus, Paraburkholderia, Variovorax and Streptomyces, the complete hnpABC cluster is only retrieved from Cupriavidus and strictly conservative in the genomes. This indicated that Cupriavidus have unique evolutionary pattern in acquiring the hnpABC to degrade TBP and its analogs, enhancing our understanding of the microbial adaptive evolution in halophenols-contaminated environment.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Suyun Fang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Jian Peng
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xin Lv
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Lingxue Xu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yan Li
- College of Life Science of Yantai University, Yantai, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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9
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Sarkar P, Maji M, Dey A. Kinetic modelling of high concentration 4-Nitrophenol biodegradation by an isolated bacterial consortium and post-treatment ecotoxicity analysis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Ke Z, Lan M, Yang T, Jia W, Gou Z, Chen K, Jiang J. A two-component monooxygenase for continuous denitration and dechlorination of chlorinated 4-nitrophenol in Ensifer sp. strain 22-1. ENVIRONMENTAL RESEARCH 2021; 198:111216. [PMID: 33971135 DOI: 10.1016/j.envres.2021.111216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
The environmental fates of chlorinated 4-nitrophenols, 2,6-dichloro-4-nitrophenol (2,6-DCNP) and 2-chloro-4-nitrophenol (2C4NP), mediated via microbial catabolism have attracted great attention due to their high toxicity and persistence in the environment. In this study, a strain of Ensifer sp. 22-1 that was capable of degrading both 2,6-DCNP and 2C4NP was isolated from a halogenated aromatic-contaminated soil sample. A gene cluster cnpBADCERM was predicted to be involved in the catabolism of 2,6-DCNP and 2C4NP based on genome sequence analysis. A two-component monooxygenase CnpAB, composed of an oxygenase component (CnpA) and a reductase component (CnpB), was confirmed to catalyze the continuous denitration and dechlorination of 2,6-DCNP and 2C4NP to 6-chlorohydroxyquinol (6-CHQ) and hydroxyquinol (HQ), respectively. Knockout of cnpA resulted in the complete loss of the capacity for strain 22-1 to degrade 2,6-DCNP and 2C4NP. Homologous modeling and docking showed that Val155~Ala159, Phe206~Pro209 and Phe446~Arg461 of CnpA participated in the formation of the FAD-binding pocket, and Arg101, Val155 and Asn447 formed hydrogen bonds with 2,6-DCNP/2C4NP in the substrate-binding pocket. This work characterized a new two-component monooxygenase for 2,6-DCNP and 2C4NP, and enriched our understanding of the degradation mechanism of chlorinated nitrophenols (CNPs) by microorganisms.
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Affiliation(s)
- Zhuang Ke
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Minjian Lan
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Tunan Yang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Weibin Jia
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhenjiu Gou
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kai Chen
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; Jiangsu Key Lab for Solid Organic Waste Utilization, 210095, Nanjing, China.
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11
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Biodegradation of aromatic pollutants meets synthetic biology. Synth Syst Biotechnol 2021; 6:153-162. [PMID: 34278013 PMCID: PMC8260767 DOI: 10.1016/j.synbio.2021.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/02/2023] Open
Abstract
Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.
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12
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Long Z, Wang X, Wang Y, Dai H, Li C, Xue Y, Deng Y, Zhang H, Yu Y, Fang H. Characterization of a novel carbendazim-degrading strain Rhodococcus sp. CX-1 revealed by genome and transcriptome analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142137. [PMID: 32916495 DOI: 10.1016/j.scitotenv.2020.142137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/21/2023]
Abstract
The persistence and ecotoxicity of carbendazim residues pose a potential risk to environmental ecology and human health. Here, a novel and highly efficient carbendazim-degrading bacterium Rhodococcus sp. CX-1, capable of utilizing carbendazim as its sole source of carbon and energy, was isolated from contaminated soil. The biodegradation characteristics and metabolic pathways were studied by mass spectrometry, genomic annotation, and transcriptome analysis. The degradation rate of carbendazim by strain CX-1 was 3.98-9.90 mg/L/h under different conditions, and the optimum degradation conditions were 40 °C and pH 7.0. The addition of carbon sources (glucose, fructose, and sucrose, 100 mg/L) could accelerate carbendazim degradation. HPLC-MS/MS identification suggested that carbendazim is first hydrolyzed into 2-aminobenzimidazole and then to 2-hydroxybenzimidazole, and is ultimately mineralized to carbon dioxide. The genome of strain CX-1 contained 6,511,628 bp nucleotides, 2 linear plasmids, 2 circular plasmids, and 6437 protein coding genes. Genome annotation and transcriptome analysis indicated that carbendazim degradation may be regulated by the degradation genes harbored in the chromosome and in plasmid 2, and two different degradation pathways of carbendazim by imidazole ring cleavage or benzene ring cleavage were predicted. This study provided new insight to reveal the biodegradation mechanism of carbendazim; furthermore, strain CX-1 is a promising bioresource for carbendazim bioremediation.
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Affiliation(s)
- Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuguo Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Yingjun Wang
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Huawei Dai
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Changhao Li
- Zibo Tobacco Limited Liability Company, Shandong, China
| | - Yongfei Xue
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yanfei Deng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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13
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Yu YH, Su JF, Shih Y, Wang J, Wang PY, Huang CP. Hazardous wastes treatment technologies. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:1833-1860. [PMID: 32866315 DOI: 10.1002/wer.1447] [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] [Received: 04/26/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
A review of the literature published in 2019 on topics related to hazardous waste management in water, soils, sediments, and air. The review covered treatment technologies applying physical, chemical, and biological principles for the remediation of contaminated water, soils, sediments, and air. PRACTICAL POINTS: This report provides a review of technologies for the management of waters, wastewaters, air, sediments, and soils contaminated by various hazardous chemicals including inorganic (e.g., oxyanions, salts, and heavy metals), organic (e.g., halogenated, pharmaceuticals and personal care products, pesticides, and persistent organic chemicals) in three scientific areas of physical, chemical, and biological methods. Physical methods for the management of hazardous wastes including general adsorption, sand filtration, coagulation/flocculation, electrodialysis, electrokinetics, electro-sorption ( capacitive deionization, CDI), membrane (RO, NF, MF), photocatalysis, photoelectrochemical oxidation, sonochemical, non-thermal plasma, supercritical fluid, electrochemical oxidation, and electrochemical reduction processes were reviewed. Chemical methods including ozone-based, hydrogen peroxide-based, potassium permanganate processes, and Fenton and Fenton-like process were reviewed. Biological methods such as aerobic, anoxic, anaerobic, bioreactors, constructed wetlands, soil bioremediation and biofilter processes for the management of hazardous wastes, in mode of consortium and pure culture were reviewed. Case histories were reviewed in four areas including contaminated sediments, contaminated soils, mixed industrial solid wastes and radioactive wastes.
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Affiliation(s)
- Yu Han Yu
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Jenn Fang Su
- Department of Chemical and Materials Engineering, Tamkang University, New Taipei City, Taiwan
| | - Yujen Shih
- Graduate Institute of Environmental Essngineering, National Sun yat-sen University, Kaohsiung, Taiwan
| | - Jianmin Wang
- Department of Civil Architectural and Environmental Engineering, Missouri University of Science & Technology, Rolla, Missouri
| | - Po Yen Wang
- Department of Civil Engineering, Widener University, Chester, Pennsylvania, USA
| | - Chin Pao Huang
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
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Zhang S, Zhang C, Sun F, Zhang Z, Zhang X, Pan H, Sun P, Zhang H. Glutathione-S-transferase (GST) catalyzes the degradation of Chlorimuron-ethyl by Klebsiella jilinsis 2N3. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:139075. [PMID: 32388135 DOI: 10.1016/j.scitotenv.2020.139075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Microbial degradation is one of the most efficient and reliable ways to remove the residues of Chlorimuron-ethyl in the environments such as soil and water. In this study, a glutathione-s-transferase (GST) gene Kj-gst was cloned from the Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3. Results showed that Kj-gst played a key role in the degradation of Chlorimuron-ethyl by strain 2N3. The mutant with gene Kj-gst knocked out showed reduced relative activity up to 70% compared with the wild type in 8 h in culture. After the knockout gene was complemented, the degradation ability of the complement mutant was essentially comparable to that of the wild type. The protein Kj-GST (50 μg) obtained from the gene Kj-gst expressed and purified in E. coli strain BL21(DE3) was capable of degrading Chlorimuron-ethyl with an initial concentration of 50 mg/mL by 42.91% under the optimal conditions (15 °C and pH = 7). Point mutation experiments on a glycine located at position 101 (Glu101) confirmed that the H site of glutathione (GSH) is the key component in Kj-GST for degrading Chlorimuron-ethyl. We conclude that Kj-GST is demonstrated for the first time to degrade Chlorimuron-ethyl with its main functional site identified at the H site of GSH, shedding insight to revealing the molecular mechanisms of degrading Chlorimuron-ethyl by Klebsiella jilinsis 2N3.
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Affiliation(s)
- Sisheng Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Zhengyi Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Peng Sun
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
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15
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Fang L, Qin H, Shi T, Wu X, Li QX, Hua R. Ortho and para oxydehalogenation of dihalophenols catalyzed by the monooxygenase TcpA and NAD(P)H:FAD reductase Fre. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121787. [PMID: 31818658 DOI: 10.1016/j.jhazmat.2019.121787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Dihalophenols such as dichlorophenols (DCPs) are important industrial chemical intermediates, but also persistent pollutants in the environment. Oxidative dehalogenation by microbes is an efficient biological method to degrade halophenols, but the mechanism is unclear yet. Cupriavidus nantongensis X1T was a type strain of genus Cupriavidus, and could degrade 2,4-dichlorophenol of 50 mg/L within 12 h. The degradation rate constant was approximately 84 fold greater than that by Bacillus endophyticus CP1R43, a well-studied 2,4-DCP-degrading bacterial strain. The genes encoding 2,4,6-trichlorophenol monooxygenase (TcpA) and NAD(P)H:FAD reductase (Fre) from strain X1T were cloned and expressed. The expressed TcpA Fre were purified. The molecular docking of TcpA with DCPs and point mutation experiments showed that the degradation activity of TcpA was associated with the length of the hydrogen bond between the substrates and the amino acids in the active pocket. DCPs were degraded via a stepwise oxidative dechlorination in a positive relationship between the oxidation ability and the electron-withdrawing potential of the p-position group. In addition, TcpA has dual dehalogenation and denitration functions. The results demonstrate that either strain X1T or TcpA and Fre can effectively dehalogenate dihalophenols, which can be useful for the treatment of dihalophenols in wastewaters and remediation of DCP-contaminated environments.
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Affiliation(s)
- Liancheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Han Qin
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States.
| | - Rimao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China.
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16
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Zang H, Wang H, Miao L, Cheng Y, Zhang Y, Liu Y, Sun S, Wang Y, Li C. Carboxylesterase, a de-esterification enzyme, catalyzes the degradation of chlorimuron-ethyl in Rhodococcus erythropolis D310-1. JOURNAL OF HAZARDOUS MATERIALS 2020; 387:121684. [PMID: 31784128 DOI: 10.1016/j.jhazmat.2019.121684] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Microbial degradation is considered to be the most acceptable method for degradation of chlorimuron-ethyl, a typical long-term residual sulfonylurea herbicide, but the underlying mechanism at the genetic and biochemical levels is unclear. In this work, the genome sequence of the chlorimuron-ethyl-degrading bacterium Rhodococcus erythropolis D310-1 was completed, and the gene clusters responsible for the degradation of chlorimuron-ethyl in D310-1 were predicted. A carboxylesterase gene, carE, suggested to be responsible for carboxylesterase de-esterification, was cloned from D310-1. CarE was expressed in Escherichia coli BL21 and purified to homogeneity. The active site of the chlorimuron-ethyl-degrading enzyme CarE and the biochemical activities of CarE were elucidated. The results demonstrated that CarE is involved in catalyzing the de-esterification of chlorimuron-ethyl. A carE deletion mutant strain, D310-1ΔcarE, was constructed, and the chlorimuron-ethyl degradation rate in the presence of 100 mg L-1 chlorimuron-ethyl within 120 h decreased from 86.5 % (wild-type strain D310-1) to 58.2 % (mutant strain D310-1ΔcarE). Introduction of the plasmid pNit-carE restored the ability of the mutant strain to utilize chlorimuron-ethyl. This study is the first to demonstrate that carboxylesterase can catalyze the de-esterification reaction of chlorimuron-ethyl and provides new insights into the mechanism underlying the degradation of sulfonylurea herbicides and a theoretical basis for the utilization of enzyme resources.
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Affiliation(s)
- Hailian Zang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Hailan Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Lei Miao
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yi Cheng
- College of Science, China Agricultural University, Beijing, 100083, PR China
| | - Yuting Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yi Liu
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Shanshan Sun
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yue Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China.
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17
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Xiang S, Lin R, Shang H, Xu Y, Zhang Z, Wu X, Zong F. Efficient Degradation of Phenoxyalkanoic Acid Herbicides by the Alkali-Tolerant Cupriavidus oxalaticus Strain X32. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3786-3795. [PMID: 32133852 DOI: 10.1021/acs.jafc.9b05061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phenoxyalkanoic acid (PAA) herbicides are mainly metabolized by microorganisms in soils, but the degraders that perform well under alkaline environments are rarely considered. Herein, we report Cupriavidus oxalaticus strain X32, which showed encouraging PAA-degradation abilities, PAA tolerance, and alkali tolerance. In liquid media, without the addition of exogenous carbon sources, X32 could completely remove 500 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) or 4-chloro-2-methylphenoxyacetic acid within 3 days, faster than that with the model degrader Cupriavidus necator JMP134. Particularly, X32 still functioned at pH 10.5. Of note, with X32 inoculation, we observed 2,4-D degradation in soils and diminished phytotoxicity to maize (Zea mays). Furthermore, potential mechanisms underlying PAA biodegradation and alkali tolerance were then analyzed by whole-genome sequencing. Three modules of tfd gene clusters involved in 2,4-D catabolism and genes encoding monovalent cation/proton antiporters involved in alkali tolerance were putatively identified. Thus, X32 could be a promising candidate for the bioremediation of PAA-contaminated sites, especially in alkaline surroundings.
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Affiliation(s)
- Sheng Xiang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Ronghua Lin
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Hongyi Shang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yong Xu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Zhenhua Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xuemin Wu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Fulin Zong
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
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18
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Min J, Xu L, Fang S, Chen W, Hu X. Microbial degradation kinetics and molecular mechanism of 2,6-dichloro-4-nitrophenol by a Cupriavidus strain. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113703. [PMID: 31818627 DOI: 10.1016/j.envpol.2019.113703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/03/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
2,6-Dichloro-4-nitrophenol (2,6-DCNP) is an emerging chlorinated nitroaromatic pollutant, and its fate in the environment is an important question. However, microorganisms with the ability to utilize 2,6-DCNP have not been reported. In this study, Cupriavidus sp. CNP-8 having been previously reported to degrade various halogenated nitrophenols, was verified to be also capable of degrading 2,6-DCNP. Biodegradation kinetics assay showed that it degraded 2,6-DCNP with the specific growth rate of 0.124 h-1, half saturation constant of 0.038 mM and inhibition constant of 0.42 mM. Real-time quantitative PCR analyses indicated that the hnp gene cluster was involved in the catabolism of 2,6-DCNP. The hnpA and hnpB gene products were purified to homogeneity by Ni-NTA chromatography. Enzymatic assays showed that HnpAB, a FAD-dependent two-component monooxygenase, converted 2,6-DCNP to 6-chlorohydroxyquinol with a Km of 3.9 ± 1.4 μM and a kcat/Km of 0.12 ± 0.04 μΜ-1 min-1. As the oxygenase component encoding gene, hnpA is necessary for CNP-8 to grow on 2,6-DCNP by gene knockout and complementation. The phylogenetic analysis showed that the hnp cluster originated from the cluster involved in the catabolism of chlorophenols rather than nitrophenols. To our knowledge, CNP-8 is the first bacterium with the ability to utilize 2,6-DCNP, and this study fills a gap in the microbial degradation mechanism of this pollutant at the molecular, biochemical and genetic levels. Moreover, strain CNP-8 could degrade three chlorinated nitrophenols rapidly from the synthetic wastewater, indicating its potential in the bioremediation of chlorinated nitrophenols polluted environments.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Lingxue Xu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; College of Life Science of Yantai University, Yantai, China
| | - Suyun Fang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Weiwei Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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19
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Zhang J, Zhao R, Cao L, Lei Y, Liu J, Feng J, Fu W, Li X, Li B. High-efficiency biodegradation of chloramphenicol by enriched bacterial consortia: Kinetics study and bacterial community characterization. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121344. [PMID: 31606710 DOI: 10.1016/j.jhazmat.2019.121344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
The risk of environmental pollution caused by chloramphenicol has necessitated special attention. Biodegradation has tremendous potential for chloramphenicol removal in the environment. Six chloramphenicol-degrading consortia were acclimated under different culture conditions to investigate their chloramphenicol biodegradation behaviors, and the bacterial community structures were comprehensively characterized. The enriched consortia CL and CH which utilized chloramphenicol as their sole carbon and energy source could thoroughly degrade 120 mg/L chloramphenicol within 5 days, and the mineralization rate reached up to 90%. Chloramphenicol biodegradation kinetics by different enriched consortia fit the modified Gompertz model or the first-order decay model (R2≥0.97). Consortia CL could almost completely degrade 1-500 mg/L CAP with a final mineralization rate of 87.8-91.7%. Chloramphenicol 3-acetate was identified to be a major intermediate of CAP biodegradation by metabolite analysis and enzyme activity assay. 16S rRNA sequencing analysis revealed that the diversities and abundances of the main genera in the enriched consortia were distinct from each other. Forty-one core OTUs belonging to 18 genera were the core bacteria which might be related to chloramphenicol biodegradation. Among them, the genera Sphingomonas, Chryseobacterium, Cupriavidus, Bradyrhizobium, Burkholderia, and Afipia with high abundance may play potential roles for chloramphenicol biodegradation.
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Affiliation(s)
- Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lijia Cao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yusha Lei
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China.
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20
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Shi T, Fang L, Qin H, Wu X, Li QX, Hua R. Minute-Speed Biodegradation of Organophosphorus Insecticides by Cupriavidus nantongensis X1 T. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13558-13567. [PMID: 31738544 DOI: 10.1021/acs.jafc.9b06157] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organophosphorus insecticides (OPs) have been widely used to control agricultural pests, which has raised concerns about OP residues in crops and the environment. In this study, we investigated the degradation kinetics and pathways of 8 OPs by Cupriavidus nantongensis X1T and identified the enzyme via gene cloning and in vitro assays. The degradation half-life of methyl parathion, triazophos, and phoxim was only 5, 9, and 43 min, respectively. It was 46 fold faster than that of triazophos by Bacillus sp. TAP-1, a well-studied triazophos-degrader. Strain X1T completely degraded not only chlorpyrifos, methyl parathion, parathion, fenitrothion, triazophos, and phoxim at 50 mg/L within 48 h but also the phenolic metabolites. This was the fastest degradation of OPs by bacterial whole cells reported thus far. The OPs were first hydrolyzed by an OP hydrolase encoded by the opdB gene in strain X1T, followed by further degradation of the metabolites. The crude enzyme maintained a full activity.
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Affiliation(s)
- Taozhong Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment , Anhui Agricultural University , Hefei , Anhui 230036 , China
| | - Liancheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment , Anhui Agricultural University , Hefei , Anhui 230036 , China
| | - Han Qin
- Key Laboratory for Agri-Food Safety, School of Resource & Environment , Anhui Agricultural University , Hefei , Anhui 230036 , China
| | - Xiangwei Wu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment , Anhui Agricultural University , Hefei , Anhui 230036 , China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering , University of Hawaii at Manoa , 1955 East-West Road , Honolulu , Hawaii 96822 , United States
| | - Rimao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment , Anhui Agricultural University , Hefei , Anhui 230036 , China
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21
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Molecular and biochemical characterization of 2-chloro-4-nitrophenol degradation via the 1,2,4-benzenetriol pathway in a Gram-negative bacterium. Appl Microbiol Biotechnol 2019; 103:7741-7750. [DOI: 10.1007/s00253-019-09994-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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Song M, Wu Y, Xu C, Wang X, Su Y. Synergistic effects of multi-active sites in silver modified Bi°-BiVO 4 toward efficient reduction of aromatic nitrobenzene. JOURNAL OF HAZARDOUS MATERIALS 2019; 368:530-540. [PMID: 30710782 DOI: 10.1016/j.jhazmat.2019.01.083] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
In this work, we report on the preparation of silver nanoparticles modified bismuth/bismuth vanadate (Bi°-BiVO4) catalyst with multi-active sites toward efficient reduction of aromatic nitrobenzene, aiming to tailor the synergistic effects of multi-active sites and specify the underlying catalytic mechanism. The as-prepared catalysts were characterized by powder X-ray diffraction, scanning electron microscopy, transmission electron microscopy, energy-dispersive X-ray and X-ray photoelectron spectroscopy. It is observed that Ag nanoparticles with diameter of ˜30 nm were anchored evenly on the surface of rod-shaped BiVO4, which offered multi-active sites to contact with the reactants effectively and transfer interfacial electron to 4-nitrophenol (4-NP) rapidly. The activity factor k of Ag/Bi°-BiVO4 for 4-NP reduction is estimated to ˜3933.4 min-1 g-1, which is much higher than that obtained from pristine BiVO4 catalyst, Bi° and noble metal Ag nanoparticles. According to the experimental results, the reaction mechanism and reaction path of 4-NP reduction for BiVO4, Bi and Ag were studied through the density functional theory (DFT) theoretical calculation, which suggested that they exhibit synergistic catalytic effect in the reaction process. This work may provide a feasible foundation for the mechanism research of semiconductor reduction to 4-nitrophenol.
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Affiliation(s)
- Meiting Song
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, PR China
| | - Yuhang Wu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, PR China
| | - Chang Xu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, PR China
| | - Xiaojing Wang
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, PR China
| | - Yiguo Su
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, PR China.
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