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Chen SF, Chen WJ, Huang Y, Wei M, Chang C. Insights into the metabolic pathways and biodegradation mechanisms of chloroacetamide herbicides. ENVIRONMENTAL RESEARCH 2023; 229:115918. [PMID: 37062473 DOI: 10.1016/j.envres.2023.115918] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023]
Abstract
Chloroacetamide herbicides are widely used around the world due to their high efficiency, resulting in increasing levels of their residues in the environment. Residual chloroacetamides and their metabolites have been frequently detected in soil, water and organisms and shown to have toxic effects on non-target organisms, posing a serious threat to the ecosystem. As such, rapid and efficient techniques that eliminate chloroacetamide residues from the ecosystem are urgently needed. Degradation of these herbicides in the environment mainly occurs through microbial metabolism. Microbial strains such as Acinetobacter baumannii DT, Bacillus altitudinis A16, Pseudomonas aeruginosa JD115, Sphingobium baderi DE-13, Catellibacterium caeni DCA-1, Stenotrophomonas acidaminiphila JS-1, Klebsiella variicola B2, and Paecilomyces marquandii can effectively degrade chloroacetamide herbicides. The degradation pathway of chloroacetamide herbicides in aerobic bacteria is mainly initiated by an N/C-dealkylation reaction, followed by aromatic ring hydroxylation and cleavage processes, whereas dechlorination is the initial reaction in anaerobic bacteria. The molecular mechanisms associated with bacterial degradation of chloroacetamide herbicides have been explored, with amidase, hydrolase, reductase, ferredoxin and cytochrome P450 oxygenase currently known to play a pivotal role in the catabolic pathways of chloroacetamides. The fungal pathway for the degradation of these herbicides is more complex with more diversified products, and the degradation enzymes and genes involved remain to be discovered. However, there are few reviews specifically summarizing the microbial degrading species and biochemical mechanisms of chloroacetamide herbicides. Here, we briefly summarize the latest progress resulting from research on microbial strain resources and enzymes involved in degradation of these herbicides and their corresponding genes. Furthermore, we explore the biochemical pathways and molecular mechanisms for biodegradation of chloroacetamide herbicides in depth, thereby providing a reference for further research on the bioremediation of such herbicides.
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Affiliation(s)
- Shao-Fang Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Wen-Juan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yaohua Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ming Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Changqing Chang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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Mahanta K, Bhattacharyya PN, Sharma AK, Rajkhowa D, Lesueur D, Verma H, Parit R, Deka J, Medhi BK, Kohli A. Residue and soil dissipation kinetics of chloroacetanilide herbicides on rice (Oryzae sativa L.) and assessing the impact on soil microbial parameters and enzyme activity. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:910. [PMID: 37392291 DOI: 10.1007/s10661-023-11513-1] [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: 12/16/2022] [Accepted: 06/11/2023] [Indexed: 07/03/2023]
Abstract
The present investigation determines the persistence of herbicides like butachlor and pretilachlor in Indian soil, and their impact on soil biological properties including microbial biomass carbon (MBC), total microbial population numbers, and enzyme activities. Butachlor was degraded faster in autumn rice soil (t1/2 of 10-13 days) than in winter rice soil (half-life of 16-18 days). The t1/2 of pretilachlor in winter rice was 12-16 days. Regardless of the seasons under cultivation, no pesticide residue was detected in rice at harvest. Herbicides induced an initial decline (0-14th days after application) in MBC (averages of 332.7-478.4 g g-1 dry soil in autumn rice and 299.6-444.3 g g-1 dry soil in winter rice), microbial populations (averages of 6.4 cfu g-1 in autumn rice and 4.6 cfu g-1 in winter rice), and phosphatase (averages of 242.6-269.3 μg p-nitrophenol g-1 dry soil h-1 in autumn rice and 188.2-212.2 μg p-nitrophenol g-1 dry soil h-1 in winter rice). The application of herbicides favored dehydrogenase (averages of 123.1-156.7 g TPF g-1 dry soil in autumn and 126.7-151.1 g TPF g-1 dry soil in winter) and urease activities (averages of 279.0-340.4 g NH4 g-1 soil 2 h-1 in autumn and 226.7-296.5 g NH4 g-1 soil 2 h-1 in winter) in rice soil at 0-14th DAA. The study suggests that applications of butachlor and pretilachlor at the rates of 1000 g ha-1 and 750 g ha-1, respectively, to control the weeds in the transplanted rice fields do not have any negative impact on the harvested rice and associated soil environment.
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Affiliation(s)
- Kaberi Mahanta
- Assam Agricultural University, Jorhat 785 013, Assam, India
| | | | | | - Dipjyoti Rajkhowa
- ICAR Research Complex for NEH Region, Nagaland Centre, Nagaland, 797106, India
| | - Didier Lesueur
- Centre de Coopération Internationale en Recherche Agronomique pour le Développent (CIRAD), UMR Eco&Sols, Hanoi, Vietnam
- Eco & Sols, Université de Montpellier (UMR), CIRAD, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut de Recherche pour le Développement (IRD), 34060 Montpellier, Montpellier SupAgro, France
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Asia hub, Common Microbial Biotechnology Platform (CMBP), Hanoi, Vietnam
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment-Deakin University, Melbourne, VIC 3125, Australia
- Chinese Academy of Tropical Agricultural Sciences, Rubber Research Institute, Haikou, China
| | - Harendra Verma
- ICAR Research Complex for NEH Region, Nagaland Centre, Nagaland, 797106, India
| | - Rajat Parit
- Assam Agricultural University, Jorhat 785 013, Assam, India
| | - Jayanta Deka
- Assam Agricultural University, Jorhat 785 013, Assam, India
| | | | - Anshuman Kohli
- Bihar Agriculture University, Sabour 813210, Bihar, India
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Liu H, Liu S, Liu H, Liu M, Yin X, Lu P, Hong Q, Liu A, Wan R, Fang S. Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159086. [PMID: 36179826 DOI: 10.1016/j.scitotenv.2022.159086] [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: 07/06/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.
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Affiliation(s)
- Hongming Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China.
| | - Shiyan Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Huijun Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Mengna Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Xiaye Yin
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Peng Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Qing Hong
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Aimin Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Rui Wan
- School of Ecology and Environment, Anhui Normal University, South of Jiuhua Road, Wuhu, Anhui 241002, China.
| | - Shangping Fang
- School of Anesthesiology, Wannan Medical College, Wuhu, Anhui, China
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Liu J, Zhao S, Wu N, Hu G, Qiu J, He J, Qiao W. Sulfate-Dependent Anaerobic Degradation of Herbicide Acetochlor by a Sulfate-Reducing Bacterium Cupidesulfovibrio sp. SRB-5. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13340-13348. [PMID: 36198124 DOI: 10.1021/acs.jafc.2c03327] [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] [Indexed: 06/16/2023]
Abstract
Acetochlor, an important chloroacetamide herbicide (CAAH) widely used in agriculture, has resulted in environmental contamination, especially of anoxic habitats. In this study, a sulfate-reducing bacterium, designated as SRB-5, was isolated from anaerobic activated sludge and was identified as Cupidesulfovibrio sp. This bacterium possesses a novel anaerobic pathway capable of degrading acetochlor. In this pathway, sulfate is first reduced to sulfide, which attacks the C-Cl bond of acetochlor and abiotically forms acetochlor-thioalcohol and dis-S-acetochlor. These further undergo microbial degradation, producing the intermediates acetochlor ethanesulfonic acid, 2-methyl-6-ethylaniline, and 2-ethylaniline. The degradation half-times of acetochlor (100 μM) by strain SRB-5 were 2.4 and 4.2 days in industrial wastewater and paddy sludge, respectively. Strain SRB-5 could also degrade alachlor, propisochlor, butachlor, pretilachlor, and metolachlor, and the degradation kinetics fit the pseudo-first-order kinetics equation. This work highlights the potential application of strain SRB-5 for the remediation of CAAHs-contaminated sites.
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Affiliation(s)
- Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Shiyu Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ningning Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Gang Hu
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Wenjing Qiao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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Liu J, Bao Y, Zhang X, Zhao S, Qiu J, Li N, He J. Anaerobic biodegradation and detoxification of chloroacetamide herbicides by a novel Proteiniclasticum sediminis BAD-10 T. ENVIRONMENTAL RESEARCH 2022; 209:112859. [PMID: 35114144 DOI: 10.1016/j.envres.2022.112859] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Chloroacetamide herbicides (CAAHs) are important herbicides that were widely used to control agricultural weeds. However, their mass applications have seriously contaminated environment, and they are toxic to living beings. CAAHs are easy to enter anoxic environments such as subsoil, wetland sediment, and groundwater, where CAAHs are mainly degraded by anaerobic organisms. To date, there are no research on the anaerobic degradation of CAAHs by pure isolate and toxicity of anaerobic metabolites of CAAHs. In this study, the anaerobic degradation kinetics and metabolites of CAAHs by an anaerobic isolate BAD-10T and the toxicity of anaerobic metabolites were studied. Isolate BAD-10T could degrade alachlor, acetochlor, propisochlor, butachlor, pretilachlor and metolachlor with the degradation kinetics fitting the pseudo-first-order kinetics equation. The degradation rates of CAAHs were significantly affected by the length of N-alkoxyalkyl groups, the shorter the N-alkoxyalkyl groups, the higher the degradation rates. Four metabolites 2-ethyl-6-methyl-N-(ethoxymethyl)-acetanilide (EMEMA), N-(2-methyl-6-ethylphenyl)-acetamide (MEPA), N-2-ethylphenyl acetamide and 2-ethyl-N-carboxyl aniline were identified during acetochlor degradation, and an anaerobic catabolic pathway of acetochlor was proposed. The toxicity of EMEMA and EMPA for zebrafish, Arabidopsis and Chlorella ellipsoidea were obviously lower than that of acetochlor, indicating that the anaerobic degradation of acetochlor by isolate BAD-10T is a detoxification process. The work reveals the anaerobic degradation kinetics and catabolic pathway of CAAHs and highlights a potential application of Proteiniclasticum sediminis BAD-10T for bioremediation of CAAHs residue-contaminated environment.
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Affiliation(s)
- Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Shiyu Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Na Li
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, Henan, 473061, PR China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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Han L, Liu T, Fang K, Li X, You X, Li Y, Wang X, Wang J. Indigenous functional microbial communities for the preferential degradation of chloroacetamide herbicide S-enantiomers in soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127135. [PMID: 34517298 DOI: 10.1016/j.jhazmat.2021.127135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/22/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
This study investigated indigenous functional microbial communities associated with the degradation of chloroacetamide herbicides acetochlor (ACE), S-metolachlor (S-MET) and their enantiomers in repeatedly treated soils. The results showed that biodegradation was the main process for the degradation of ACE, S-MET and their enantiomers. Eight dominant bacterial genera associated with the degradation were found: Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, Mycobacterium, Burkholderia, Afipia, and Kribbella. The S-enantiomers of ACE and S-MET were preferentially degraded, which mainly relied on Amycolatopsis, Saccharomonospora and Kribbella for the ACE S-enantiomer and Amycolatopsis and Saccharomonospora for the S-MET S-enantiomer. Importantly, the relative abundances of Amycolatopsis and Saccharomonospora increased by 146.3%-4467.2% in the S-enantiomer treatments of ACE and S-MET compared with the control, which were significantly higher than that in the corresponding R-enantiomer treatments (25.3%-4168.2%). Both metagenomic and qPCR analyses demonstrated that four genes, ppah, alkb, benA, and p450, were the dominant biodegradation genes (BDGs) potentially involved in the preferential degradation of the S-enantiomers of ACE and S-MET. Furthermore, network analysis suggested that Amycolatopsis, Saccharomonospora, Mycoplasma, Myroides, and Mycobacterium were the potential hosts of these four BDGs. Our findings indicated that Amycolatopsis and Saccharomonospora might play pivotal roles in the preferential degradation of the S-enantiomers of ACE and S-MET.
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Affiliation(s)
- Lingxi Han
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China
| | - Tong Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China
| | - Kuan Fang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China
| | - Xianxu Li
- College of Resources and Environment, Key Laboratory of Agricultural Environment, Shandong Agricultural University, Tai'an 271000, PR China
| | - Xiangwei You
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China
| | - Yiqiang Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China
| | - Xiuguo Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China.
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment, Shandong Agricultural University, Tai'an 271000, PR China.
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Rong L, Wu X, Xu J, Dong F, Liu X, Xu H, Cao J, Zheng Y. Clomazone improves the interactions between soil microbes and affects C and N cycling functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144730. [PMID: 33736380 DOI: 10.1016/j.scitotenv.2020.144730] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Clomazone, a widely used herbicide, is mainly used in soybean fields. We previously found that clomazone alters Proteobacteria and Nitrospirae abundances and also alters urease activity, which result in changes in NH4+ and NO3- contents in soil nitrogen cycling. It remains unknown, however, how the co-occurrence patterns of species and functions of soil ecosystems change in response to clomazone applications in soil. We designed a 3-month greenhouse experiment to investigate soil microorganism dynamics in response to clomazone. Clomazone was applied at three doses (e.g., T1, T10, T100), which significantly increased bacterial abundance at days 15 and 60. Fungal abundance was stimulated at day 30 in T10-treated soils, whereas fungal abundances decreased in T100-treated soils at day 15. Clomazone altered bacterial and fungal community structures. Network analyses showed more complex and highly connected microbial communities in clomazone-treated soils. Moreover, an Acidobacteria-dominated cluster was identified within each network of clomazone-treated soils. Clomazone applied at the recommended rate decreased the functional groups that were associated with denitrification and hydrogen oxidation at days 15 and 60, and enhanced photoheterotrophy from days 30 to 60. High clomazone inputs increased trophic types (e.g., chemoheterotrophy, phototrophy, photoautotrophy and cyanobacteria) and C cycling functional groups (e.g., fermentation and cellulolysis). The half-life of clomazone ranged from 40.1 to 93.5 days in three cases. Our results provide important information for use of this herbicide.
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Affiliation(s)
- Lili Rong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hanqing Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junli Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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9
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Liu J, Zhang X, Xu J, Qiu J, Zhu J, Cao H, He J. Anaerobic biodegradation of acetochlor by acclimated sludge and its anaerobic catabolic pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141122. [PMID: 32810802 DOI: 10.1016/j.scitotenv.2020.141122] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/10/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
Acetochlor is a chloroacetamide herbicide that has been widely used for weed control in recent decades. The contamination from its residue in the environment has raised major serious concerns. The aerobic degradation of acetochlor has been well studied; however, little is known regarding its anaerobic degradation. In the study, anaerobic sludge with high acetochlor degradation efficiency was obtained by pressure acclimation in a continuous flow anaerobic reactor. The acetochlor degradation dynamics followed a first-order kinetic reaction equation. The acclimated sludge could degrade six chloroacetamide herbicides with the degradation efficiencies observed as alachlor > acetochlor > propisochlor > butachlor > pretilachlor > metolachlor, and the N-alkoxyalkyl structure of these herbicides significantly affected their biodegradability. Five metabolites, 2-ethyl-6-methyl-N-(ethoxymethyl)-acetanilide, N-(2-methyl-6-ethylphenyl) acetamide, N-2-ethylphenyl acetamide, N-2-ethylphenyl formamide and 2-ethyl-N-carboxyl aniline were identified, and a putative anaerobic acetochlor degradation pathway, initiated by dechlorination, was subsequently proposed. During acclimation, the community diversity of both eubacteria and archaea in the anaerobic sludge decreased, while the abundance of microbes belonging to genera Sporomusa, Sporobacterium, Dechloromonas, Azotobacter and Methanobacterium were significantly increased and dominated the acclimated sludge, and showing a positive correlation with the acetochlor degradation capacity. These findings should be valuable to elucidate the mechanisms associated with the anaerobic catabolism of acetochlor and facilitate the engineering application of anaerobic treatment for removing acetochlor from wastewater.
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Affiliation(s)
- Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Jianyi Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Jianchun Zhu
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Chenprakhon P, Wongnate T, Chaiyen P. Monooxygenation of aromatic compounds by flavin-dependent monooxygenases. Protein Sci 2020; 28:8-29. [PMID: 30311986 DOI: 10.1002/pro.3525] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Many flavoenzymes catalyze hydroxylation of aromatic compounds especially phenolic compounds have been isolated and characterized. These enzymes can be classified as either single-component or two-component flavin-dependent hydroxylases (monooxygenases). The hydroxylation reactions catalyzed by the enzymes in this group are useful for modifying the biological properties of phenolic compounds. This review aims to provide an in-depth discussion of the current mechanistic understanding of representative flavin-dependent monooxygenases including 3-hydroxy-benzoate 4-hydroxylase (PHBH, a single-component hydroxylase), 3-hydroxyphenylacetate 4-hydroxylase (HPAH, a two-component hydroxylase), and other monooxygenases which catalyze reactions in addition to hydroxylation, including 2-methyl-3-hydroxypyridine-5-carboxylate oxygenase (MHPCO, a single-component enzyme that catalyzes aromatic-ring cleavage), and HadA monooxygenase (a two-component enzyme that catalyzes additional group elimination reaction). These enzymes have different unique structural features which dictate their reactivity toward various substrates and influence their ability to stabilize flavin intermediates such as C4a-hydroperoxyflavin. Understanding the key catalytic residues and the active site environments important for governing enzyme reactivity will undoubtedly facilitate future work in enzyme engineering or enzyme redesign for the development of biocatalytic methods for the synthesis of valuable compounds.
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Affiliation(s)
- Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 14000, Thailand
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11
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Cheng M, Xing Z, Lu L, Chen F, He J, Huang X. A plasmid-based genomic screening system for transcriptional regulators of non-adjacent xenobiotic catabolism genes. Appl Microbiol Biotechnol 2019; 104:1163-1174. [PMID: 31822983 DOI: 10.1007/s00253-019-10268-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/11/2019] [Accepted: 11/22/2019] [Indexed: 12/01/2022]
Abstract
Bacteria play an important role in the catabolism of environmental xenobiotics. The study of transcriptional regulation has greatly enhanced our understanding of the molecular mechanisms associated with these processes. However, genes encoding transcription factors (TFs) for xenobiotic catabolism are usually not located in the immediate vicinity of the catabolic genes that they regulate; therefore, functional identification of these TFs is difficult. Significantly modified from a metagenome screening method substrate-induced gene expression (SIGEX), here we propose a synthetic pSRGFP-18 plasmid-based tool as a TF reporter system. In short, two multiple cloning sites (MCS) were designed; one in front of an egfp reporter gene was constructed for promoter insertion, and the other MCS was used for shotgun cloning of genomic DNA. Based on the regulatory relationship between TFs and the promoter of their associated catabolic genes, this approach allowed us to screen for TF genes using a genome shotgun approach. This system performed well when testing the known operons. Following statistical analysis of known catabolic operons in Escherichia coli and Bacillus subtilis, the suggested region of the target promoter for this system was from - 250 to + 150. Furthermore, to broaden the applicability of this plasmid, a series of pSRGFP-18 and pBBR1-based pSRGFP-X plasmids were constructed, which had broad host ranges and contained different antibiotic markers. This study outlines a powerful tool to enable functional identification of TFs for bacterial xenobiotic catabolism.
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Affiliation(s)
- Minggen Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ziyu Xing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xing Huang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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12
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Cheng M, Yan X, He J, Qiu J, Chen Q. Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6. Arch Microbiol 2019; 201:907-918. [PMID: 30997539 DOI: 10.1007/s00203-019-01660-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin Yan
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jian He
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jiguo Qiu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Qing Chen
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. .,College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China.
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13
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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14
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Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation in Sphingomonas sp. Strain CDS-1. Appl Environ Microbiol 2018; 84:AEM.00805-18. [PMID: 29884759 DOI: 10.1128/aem.00805-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 01/29/2023] Open
Abstract
Carbofuran, a broad-spectrum systemic insecticide, has been extensively used for approximately 50 years. Diverse carbofuran-degrading bacteria have been described, among which sphingomonads have exhibited an extraordinary ability to catabolize carbofuran; other bacteria can only convert carbofuran to carbofuran phenol, while all carbofuran-degrading sphingomonads can degrade both carbofuran and carbofuran phenol. However, the genetic basis of carbofuran catabolism in sphingomonads has not been well elucidated. In this work, we sequenced the draft genome of Sphingomonas sp. strain CDS-1 that can transform both carbofuran and carbofuran phenol but fails to grow on them. On the basis of the hypothesis that the genes involved in carbofuran catabolism are highly conserved among carbofuran-degrading sphingomonads, two such genes, cehACDS-1 and cfdCCDS-1, were predicted from the 84 open reading frames (ORFs) that share ≥95% nucleic acid similarities between strain CDS-1 and another sphingomonad Novosphingobium sp. strain KN65.2 that is able to mineralize the benzene ring of carbofuran. The results of the gene knockout, genetic complementation, heterologous expression, and enzymatic experiments reveal that cehACDS-1 and cfdCCDS-1 are responsible for the conversion of carbofuran and carbofuran phenol, respectively, in strain CDS-1. CehACDS-1 hydrolyzes carbofuran to carbofuran phenol. CfdCCDS-1, a reduced flavin mononucleotide (FMNH2)- or reduced flavin adenine dinucleotide (FADH2)-dependent monooxygenase, hydroxylates carbofuran phenol at the benzene ring in the presence of NADH, FMN/FAD, and the reductase CfdX. It is worth noting that we found that carbaryl hydrolase CehAAC100, which was previously demonstrated to have no activity toward carbofuran, can actually convert carbofuran to carbofuran phenol, albeit with very low activity.IMPORTANCE Due to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation in Sphingomonas sp. strain CDS-1. We speculate that the close homologues cehA and cfdC are highly conserved among other carbofuran-degrading sphingomonads and play the same roles as those described here. These findings deepen our understanding of the microbial degradation mechanism of carbofuran and lay a foundation for the better use of microbes to remediate carbofuran contamination.
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Du P, Wu X, Xu J, Dong F, Liu X, Zheng Y. Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling. JOURNAL OF HAZARDOUS MATERIALS 2018; 353:204-213. [PMID: 29674095 DOI: 10.1016/j.jhazmat.2018.04.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg-1) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19-61.83 d in all cases. Bacterial abundance increased 1.12-5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again. Linear discriminant analysis effect size indicated that Sphingomonas and Xanthomonadaceae were the predominant species on day 7 and 15 in TFL treatments. N2-fixing bacteria were initially increased, then decreased, and then recovered, and it was positively correlated with NH4+-N content. Compared with the control, ammonia-oxidizing bacteria were decreased by 25.51-92.63%, ammonia-oxidizing archaea were decreased by 17.12-85.21% (except day 7), and the NO3--N concentration was also inhibited. In contrast to bacteria, fungal abundance was inhibited without any observable effects on fungal diversity or community structure. These results suggest that TFL impacts soil bacterial community and alters functional microorganisms involved in soil N processing.
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Affiliation(s)
- Pengqiang Du
- College of Chemistry, Central China Normal University, No. 152 Luoyu Road, Wuhan, 430079, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| | - Yongquan Zheng
- College of Chemistry, Central China Normal University, No. 152 Luoyu Road, Wuhan, 430079, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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Wang H, Jiang K, Zhu Z, Jiang W, Yang Z, Zhu S, Qiu J, Yan X, He J, He Q, Hong Q. Optimization of fed-batch fermentation and direct spray drying in the preparation of microbial inoculant of acetochlor-degrading strain Sphingomonas sp. DC-6. 3 Biotech 2018; 8:294. [PMID: 29963354 DOI: 10.1007/s13205-018-1324-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022] Open
Abstract
Microbial inoculant preparation is a prerequisite for its application in large-scale bioremediation. In the present study, Sphingomonas sp. DC-6, an efficient acetochlor-degrading strain, was used to investigate the process of preparing the inoculant. Optimization of submerged fermentation (SmF) by response surface methodology (RSM) resulted in a first 22% increase in biomass of liquid inoculant. Then, a biomass increase of 2.18 times with 14.58% shortened incubation period was further obtained in optimized medium using a 7.5-l bioreactor. However, less than 0.4% viable cells in liquid inoculant survived after 180-days storage. Thus, optimized spray drying conditions were subsequently employed for the production of high viability powder (2.11 × 1012 cfu g- 1 powder) without additive and its survival ratio (SR) after 180-days storage was still maintained at 90.5%. Both the 180-days stored powder and the original powder showed the same degradation performance, being able to completely degrade 200 mg l- 1 acetochlor within 48 h. This study demonstrated that strain DC-6 was suitable for industrial production of bacteria powder and provided a potential approach for the preparation of pesticide-degrading microbial inoculant.
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Affiliation(s)
- Hui Wang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Kun Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Ziwei Zhu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Wankui Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Zhangong Yang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Shijun Zhu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Jiguo Qiu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Xin Yan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Jian He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Qin He
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
| | - Qing Hong
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 People's Republic of China
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Ito K, Takagi K, Matsushima Y, Iwasaki A, Tanaka N, Kanesaki Y, Martin-Laurent Martin-Laurent FF, Igimi S. Identification of the novel hcbB operon catalyzing the dechlorination of pentachlorophenol in the Gram-positive bacterium Nocardioides sp. strain PD653. JOURNAL OF PESTICIDE SCIENCE 2018; 43:124-131. [PMID: 30363388 PMCID: PMC6173144 DOI: 10.1584/jpestics.d17-089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While pcp genes are well known in Gram-negative bacteria to code for the enzymes responsible for pentachlorophenol (C6HCl5O; PCP) degradation, little is known about PCP-degrading genes in Gram-positive bacteria. Here we describe a novel gene operon possibly responsible for catalyzing the degradation of PCP in the Gram-positive bacterium Nocardioides sp. strain PD653, which is capable of mineralizing hexachlorobenzene (C6Cl6; HCB) via PCP. Transcriptome analysis based on RNA-Seq revealed overexpressed genes in strain PD653 following exposure to HCB. Based on in silico annotation, three open reading frames (ORFs) were selected as biodegrading enzyme candidates. Recombinant E. coli cells expressing candidate genes degraded approximately 9.4 µmol L-1 PCP in 2 hr. Therefore, we designated these genes as hcbB1, hcbB2, and hcbB3. Interestingly, PCP-degrading activity was recorded when hcbB3 was coexpressed with hcbB1 or hcbB2, and the function of HcbB3 was expected to be similar to chlorophenol 4-monooxygenase (TftD).
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Affiliation(s)
- Koji Ito
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
| | - Kazuhiro Takagi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
- To whom correspondence should be addressed. E-mail:
| | | | - Akio Iwasaki
- Juntendo Medical Technology Innovation Center, Juntendo University
| | - Naoto Tanaka
- Department of Molecular Microbiology, Tokyo University of Agriculture
| | - Yu Kanesaki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture
| | | | - Shizunobu Igimi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
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18
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Li N, Yao L, He Q, Qiu J, Cheng D, Ding D, Tao Q, He J, Jiang J. 3,6-Dichlorosalicylate Catabolism Is Initiated by the DsmABC Cytochrome P450 Monooxygenase System in Rhizorhabdus dicambivorans Ndbn-20. Appl Environ Microbiol 2018; 84:e02133-17. [PMID: 29196293 PMCID: PMC5795090 DOI: 10.1128/aem.02133-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
The degradation of the herbicide dicamba is initiated by demethylation to form 3,6-dichlorosalicylate (3,6-DCSA) in Rhizorhabdusdicambivorans Ndbn-20. In the present study, a 3,6-DCSA degradation-deficient mutant, Ndbn-20m, was screened. A cluster, dsmR1DABCEFGR2, was lost in this mutant. The cluster consisted of nine genes, all of which were apparently induced by 3,6-DCSA. DsmA shared 30 to 36% identity with the monooxygenase components of reported three-component cytochrome P450 systems and formed a monophyletic branch in the phylogenetic tree. DsmB and DsmC were most closely related to the reported [2Fe-2S] ferredoxin and ferredoxin reductase, respectively. The disruption of dsmA in strain Ndbn-20 resulted in inactive 3,6-DCSA degradation. When dsmABC, but not dsmA alone, was introduced into mutant Ndbn-20m and Sphingobium quisquiliarum DC-2 (which is unable to degrade salicylate and its derivatives), they acquired the ability to hydroxylate 3,6-DCSA. Single-crystal X-ray diffraction demonstrated that the DsmABC-catalyzed hydroxylation occurred at the C-5 position of 3,6-DCSA, generating 3,6-dichlorogentisate (3,6-DCGA). In addition, DsmD shared 51% identity with GtdA (a gentisate and 3,6-DCGA 1,2-dioxygenase) from Sphingomonas sp. strain RW5. However, unlike GtdA, the purified DsmD catalyzed the cleavage of gentisate and 3-chlorogentisate but not 6-chlorogentisate or 3,6-DCGA in vitro Based on the bioinformatic analysis and gene function studies, a possible catabolic pathway of dicamba in R. dicambivorans Ndbn-20 was proposed.IMPORTANCE Dicamba is widely used to control a variety of broadleaf weeds and is a promising target herbicide for the engineering of herbicide-resistant crops. The catabolism of dicamba has thus received increasing attention. Bacteria mineralize dicamba initially via demethylation, generating 3,6-dichlorosalicylate. However, the catabolism of 3,6-dichlorosalicylate remains unknown. In this study, we cloned a gene cluster, dsmR1DABCEFGR2, involved in 3,6-dichlorosalicylate degradation from R. dicambivorans Ndbn-20, demonstrated that the cytochrome P450 monooxygenase system DsmABC was responsible for the 5-hydroxylation of 3,6-dichlorosalicylate, and proposed a dicamba catabolic pathway. This study provides a basis to elucidate the catabolism of dicamba and has benefits for the ecotoxicological study of dicamba. Furthermore, the hydroxylation of salicylate has been previously reported to be catalyzed by single-component flavoprotein or three-component Rieske non-heme iron oxygenase, whereas DsmABC was the only cytochrome P450 monooxygenase system hydroxylating salicylate and its methyl- or chloro-substituted derivatives.
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Affiliation(s)
- Na Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Li Yao
- School of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Qin He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Dan Cheng
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Derong Ding
- Beijing DBN Biotech Co., Ltd., Beijing, China
| | - Qing Tao
- Beijing DBN Biotech Co., Ltd., Beijing, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiandong Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1. Appl Environ Microbiol 2017; 83:AEM.01490-17. [PMID: 28939603 DOI: 10.1128/aem.01490-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/13/2017] [Indexed: 11/20/2022] Open
Abstract
Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD+ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis.IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism.
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Complete Genome Sequence of Sphingobium baderi DE-13, an Alkyl-Substituted Aniline-Mineralizing Bacterium. Curr Microbiol 2017; 75:27-31. [DOI: 10.1007/s00284-017-1346-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/18/2017] [Indexed: 10/19/2022]
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