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Singh NS, Mukherjee I. Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34902-6. [PMID: 39240431 DOI: 10.1007/s11356-024-34902-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024]
Abstract
The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network (BN), quantitative structure-activity relationship-density functional theory (QSAR-DFT), artificial neural network (ANN), molecular docking (MD), and molecular dynamics stimulation (MS) of PCB biodegradation, i.e., PCB-10, PCB-28, PCB-52, PCB-138, PCB-153, and PCB-180 in the soil system using fungi isolated from the transformer oil-contaminated sites. Results revealed that the efficacy of PCB biodegradation best fits the first-order kinetics (R2 ≥ 0.93). The consortium treatment (29.44-74.49%) exhibited more efficient degradation of PCBs than those of Aspergillus tamarii sp. MN69 (27.09-71.25%), Corynespora cassiicola sp. MN69 (23.76-57.37%), and Corynespora cassiicola sp. MN70 (23.09-54.98%). 3'-Methoxy-2, 4, 4'-trichloro-biphenyl as an intermediate derivative was detected in the fungal consortium treatment. The BN analysis predicted that the biodegradation efficiency of PCBs ranged from 11.6 to 72.9%. The ANN approach showed the importance of chemical descriptors in decreasing order, i.e., LUMO > MW > IP > polarity no. > no. of chlorine > Wiener index > Zagreb index > HOMU > Pogliani index > APE in PCB removal. Furthermore, the QSAR-DFT model between the chemical descriptors and rate constant (log K) exhibited a high fit and good robustness of R2 = 99.12% in predicting ability. The MD and MS analyses showed the lowest binding energy through normal mode analysis (NMA), implying stability in the interactions of the docked complexes. These findings provide crucial insights for devising strategies focused on natural attenuation, holding substantial potential for mitigating PCB contamination within the environment.
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Affiliation(s)
- Ningthoujam Samarendra Singh
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - Irani Mukherjee
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India.
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2
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Kou L, Chen H, Zhang X, Liu S, Zhang B, Zhu H, Du Z. Enhanced degradation of phthalate esters (PAEs) by biochar-sodium alginate immobilised Rhodococcus sp. KLW-1. ENVIRONMENTAL TECHNOLOGY 2024; 45:3367-3380. [PMID: 37191443 DOI: 10.1080/09593330.2023.2215456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
In this study, a new strain of bacteria, named Rhodococcus sp. KLW-1, was isolated from farmland soil contaminated by plastic mulch for more than 30 years. To improve the application performance of free bacteria and find more ways to use waste biochar, KLW-1 was immobilised on waste biochar by sodium alginate embedding method to prepare immobilised pellet. Response Surface Method (RSM) predicted that under optimal conditions (3% sodium alginate, 2% biochar and 4% CaCl2), di (2-ethylhexyl) phthalate (DEHP) degradation efficiency of 90.48% can be achieved. Under the adverse environmental conditions of pH 5 and 9, immobilisation increased the degradation efficiency of 100 mg/L DEHP by 16.42% and 11.48% respectively, and under the high-stress condition of 500 mg/L DEHP concentration, immobilisation increased the degradation efficiency from 71.52% to 91.56%, making the immobilised pellets have strong stability and impact load resistance to environmental stress. In addition, immobilisation also enhanced the degradation efficiency of several phthalate esters (PAEs) widely existing in the environment. After four cycles of utilisation, the immobilised particles maintained stable degradation efficiency for different PAEs. Therefore, immobilised pellets have great application potential for the remediation of the actual environment.
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Affiliation(s)
- Liangwei Kou
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Hanyu Chen
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Xueqi Zhang
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Shaoqin Liu
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Huina Zhu
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
| | - Zhimin Du
- School of Environmental Engineering, Henan University of Technology, Zhengzhou, People's Republic of China
- Henan International Joint Laboratory of Environmental Pollution, Remediation and Grain Quality Security, Zhengzhou, People's Republic of China
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Wu Y, Zhu M, Ouyang X, Qi X, Guo Z, Yuan Y, Dang Z, Yin H. Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1. CHEMOSPHERE 2024; 356:141921. [PMID: 38588902 DOI: 10.1016/j.chemosphere.2024.141921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.
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Affiliation(s)
- Yuxuan Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofang Ouyang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhanyu Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China.
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4
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Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. CHEMOSPHERE 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [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: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
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5
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Hao P, Lv Z, Pan H, Zhang J, Wang L, Zhu Y, Basang W, Gao Y. Characterization and low-temperature biodegradation mechanism of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9. ENVIRONMENTAL RESEARCH 2024; 240:117513. [PMID: 37890824 DOI: 10.1016/j.envres.2023.117513] [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: 05/05/2023] [Revised: 10/16/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
Steroidal estrogens residues in the environment can be a serious hazard to humans and animals and has been listed as group 1 carcinogens by World Health Organization (WHO). Microbial degradation is one of the effective strategies for the removal of such contaminants. In this study, a low-temperature degrading bacterial strain (Rhodococcus sp. RCBS9) was isolated from the soil of a dairy farm for 17β-estradiol (E2) degradation. The strain RCBS9 exhibited an efficient degradation potential at low temperatures. To lean how different factors influence E2 degradation, we have found a major role of intracellular enzymes in E2 degradation. Genomic and metabolomic analyses have suggested potential degradation genes and four metabolic pathways. These findings provide valuable strain resources for the low temperature bioremediation of E2 contamination and insights into E2 biodegradation mechanism.
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Affiliation(s)
- Peng Hao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Zongshuo Lv
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Hanyu Pan
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Jingyi Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China
| | - Lixia Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Yunhang Gao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118, China.
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6
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Zhou H, Yin H, Guo Z, Zhu M, Qi X, Dang Z. Methanol promotes the biodegradation of 2,2',3,4,4',5,5'-heptachlorobiphenyl (PCB 180) by the microbial consortium QY2: Metabolic pathways, toxicity evaluation and community response. CHEMOSPHERE 2023; 322:138206. [PMID: 36828105 DOI: 10.1016/j.chemosphere.2023.138206] [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: 08/29/2022] [Revised: 12/24/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
As one of the most frequently detected PCB congeners in human adipose tissue, 2,2',3,4,4',5,5'-heptachlorobiphenyl (PCB 180) has attracted much attention. However, PCB 180 is difficult to be directly utilized by microorganisms due to its hydrophobicity and obstinacy. Herein, methanol (5 mM) as a co-metabolic carbon source significantly stimulated the degradation performance of microbial consortium QY2 for PCB 180 (51.9% higher than that without methanol addition). Six metabolic products including low-chlorinated PCBs and chlorobenzoic acid were identified during co-metabolic degradation, denoting that PCB 180 was metabolized via dechlorination, hydroxylation and ring-opening pathways. The oxidative stress and apoptosis induced by PCB 180 were dose-dependent, but the addition of methanol effectively promoted the tolerance of consortium QY2 to resist unfavorable environmental stress. Additionally, the significant reduction of intracellular reactive oxygen species (ROS) and enhancement of cell viability during methanol co-metabolic degradation proved that the degradation was a detoxification process. The microbial community and network analyses suggested that the potential PCB 180 degrading bacteria in the community (e.g., Achromobacter, Cupriavidus, Methylobacterium and Sphingomonas) and functional abundance of metabolic pathways were selectively enriched by methanol, and the synergies among species whose richness increased after methanol addition might dominate the degradation process. These findings provide new insights into the biodegradation of PCB 180 by microbial consortium.
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Affiliation(s)
- Heyang Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China.
| | - Zhanyu Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
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7
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Chen J, Tong T, Yang Y, Ke Y, Chen X, Xie S. In-situ active Bisphenol A-degrading microorganisms in mangrove sediments. ENVIRONMENTAL RESEARCH 2022; 206:112251. [PMID: 34695429 DOI: 10.1016/j.envres.2021.112251] [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: 09/09/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Bisphenol A (BPA), as both an endocrine disrupting compound and an important industrial material, is broadly distributed in coastal regions and may cause adverse effects on mangrove ecosystems. Although many BPA degraders have been isolated from various environments, the in-situ active BPA-degrading microorganisms in mangrove ecosystem are still unknown. In this study, DNA-based stable isotope probing in combination with high-throughput sequencing was adopted to pinpoint the microbes actually involved in BPA metabolism in mangrove sediments. Five bacterial genera were speculated to be associated with BPA degradation based on linear discriminant analysis (LDA) effect size (LEfSe) analysis, including Truepera, Methylobacterium, Novosphingobium, Rhodococcus and Rhodobacter. The in-situ BPA degraders were different between mudflat and forest sediments. The Shannon index of microbes in heavy fractions was significantly lower than that in light fractions. Besides, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) demonstrated that the functional genes relevant to cytochrome P450, benzoate degradation, bisphenol degradation and citrate cycle were up-regulated significantly in in-situ BPA-degrading microbes. These findings greatly expanded the knowledge of indigenous BPA metabolic microorganisms in mangrove ecosystems.
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Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yuyin Yang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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8
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Yu C, Wang H, Blaustein RA, Guo L, Ye Q, Fu Y, Fan J, Su X, Hartmann EM, Shen C. Pangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151141. [PMID: 34688761 DOI: 10.1016/j.scitotenv.2021.151141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Environmental bacteria contain a wealth of untapped potential in the form of biodegradative genes. Leveraging this potential can often be confounded by a lack of understanding of fundamental survival strategies, like dormancy, for environmental stress. Investigating bacterial dormancy-to-degradation relationships enables improvement of bioremediation. Here, we couple genomic and functional assessment to provide context for key attributes of the organic pollutant-degrading strain Rhodococcus biphenylivorans TG9. Whole genome sequencing, pangenome analysis and functional characterization were performed to elucidate important genes and gene products, including antimicrobial resistance, dormancy, and degradation. Rhodococcus as a genus has strong potential for degradation and dormancy, which we demonstrate using R. biphenylivorans TG9 as a model. We identified four Resuscitation-promoting factor (Rpf) encoding genes in TG9 involved in dormancy and resuscitation. We demonstrate that R. biphenylivorans TG9 grows on fourteen typical organic pollutants, and exhibits a robust ability to degrade biphenyl and several congeners of polychlorinated biphenyls. We further induced TG9 into a dormant state and demonstrated pronounced differences in morphology and activity. Together, these results expand our understanding of the genus Rhodococcus and the relationship between dormancy and biodegradation in the presence of environmental stressors.
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Affiliation(s)
- Chungui Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hui Wang
- College of Eco-Environmental Engineering, Guizhou Minzu University, Guiyang, Guizhou, China; Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ryan Andrew Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Li Guo
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qi Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiahui Fan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, Zhejiang, China; Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Erica Marie Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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9
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Yu C, Armengaud J, Blaustein RA, Chen K, Ye Z, Xu F, Gaillard JC, Qin Z, Fu Y, Hartmann EM, Shen C. Antibiotic tolerance and degradation capacity of the organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9 T. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127712. [PMID: 34865898 DOI: 10.1016/j.jhazmat.2021.127712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/14/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics are ubiquitous in soil due to natural ecological competition, as well as emerging contaminants due to anthropogenic inputs. Under environmental factors like antibiotic stress, some bacteria, including those that degrade environmental pollutants, can enter a dormant state as a survival strategy, thereby limiting their metabolic activity and function. Dormancy has a critical influence on the degradative activity of bacteria, dramatically decreasing the rate at which they transform organic pollutants. To better understand this phenomenon in environmental pollutant-degrading bacteria, we investigated dormancy transitions induced with norfloxacin in Rhodococcus biphenylivorans TG9T using next-generation proteomics, proteogenomics, and additional experiments. Our results suggest that exposure to norfloxacin inhibited DNA replication, which led to damage to the cell. Dormant cells then likely triggered DNA repair, particularly homologous recombination, for continued survival. The results also indicated that substrate transport (ATP-binding cassette transporter), ATP production, and the tricarboxylic acid (TCA) cycle were repressed during dormancy, and degradation of organic pollutants was down-regulated. Given the widespread phenomenon of dormancy among bacteria involved in pollutant removal systems, this study improves our understanding of possible implications of antibiotic survival strategies on biotransformation of mixtures containing antibiotics as well as other organics.
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Affiliation(s)
- Chungui Yu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Ryan Andrew Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Kezhen Chen
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Zhe Ye
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Fengjun Xu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France
| | - Zhihui Qin
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Yulong Fu
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China
| | - Erica Marie Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
| | - Chaofeng Shen
- Zhejiang University, Department of Environmental Engineering, College of Environmental and Resource Sciences, Hangzhou 310058, Zhejiang, China.
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Dávila Costa JS, Guerrero DS, Romero CM. Streptomyces: connecting red-nano and grey biotechnology fields. Crit Rev Microbiol 2021; 48:565-576. [PMID: 34651534 DOI: 10.1080/1040841x.2021.1991272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Anthropogenic activities are often related to the occurrence of simultaneous contaminations with heavy metals and toxic organic compounds. In addition, the increasing demand for food, clothing, and technology has increased the worldwide contamination level. Although it is not fully demonstrated, the high level of contamination in association with the indiscriminate use of antibiotics, led to the appearance of multi-resistant pathogenic microorganisms. Grey and red biotechnologies try to counteract the negative effects of pollution and antimicrobial resistance respectively. Streptomyces is well known in the field of biotechnology. In this review, we discussed the potential of these bacteria to deal with organic and inorganic pollutants and produce nanostructures with antimicrobial activity. To our knowledge, this is the first work in which a biotechnological bacterial genus such as Streptomyces is revised in two different fields of global concern, contamination, and multi-drugs resistant microorganisms.
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Affiliation(s)
| | | | - Cintia Mariana Romero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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Kuhl T, Chowdhury SP, Uhl J, Rothballer M. Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits. Front Microbiol 2021; 12:708605. [PMID: 34489897 PMCID: PMC8416521 DOI: 10.3389/fmicb.2021.708605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/26/2021] [Indexed: 11/24/2022] Open
Abstract
Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.
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Affiliation(s)
- Theresa Kuhl
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jenny Uhl
- Research Unit Analytical Biogeochemistry, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
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