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Gao J, Ali MY, Kamaraj Y, Zhang Z, Weike L, Sethupathy S, Zhu D. A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics. Microbiol Res 2024; 287:127835. [PMID: 39032264 DOI: 10.1016/j.micres.2024.127835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.
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Affiliation(s)
- Jiayue Gao
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mohamed Yassin Ali
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Yoganathan Kamaraj
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zhenghao Zhang
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Li Weike
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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Wu X, Tang Y, Amanze C, Peng J, Yu R, Li J, Shen L, Liu Y, Zeng W. Fabrication and optimization of bioelectrochemical system using tetracycline-degrading bacterial strains for antibiotic wastewater treatment. BIORESOURCE TECHNOLOGY 2024; 407:131096. [PMID: 38986881 DOI: 10.1016/j.biortech.2024.131096] [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: 03/13/2024] [Revised: 06/19/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
In this study, a microbial fuel cell was constructed using Raoultella sp. XY-1 to efficiently degrade tetracycline (TC) and assess the effectiveness of the electrochemical system. The degradation rate reached 83.2 ± 1.8 % during the 7-day period, in which the system contained 30 mg/L TC, and the degradation pathway and intermediates were identified. Low concentrations of TC enhanced anodic biofilm power production, while high concentrations of TC decreased the electrochemical activity of the biofilm, extracellular polymeric substances, and enzymatic activities associated with electron transfer. Introducing electrogenic bacteria improved power generation efficiency. A three-strain hybrid system was fabricated using Castellaniella sp. A3, Castellaniella sp. A5 and Raoultella sp. XY-1, leading to the enhanced TC degradation rate of 90.4 % and the increased maximum output voltage from 200 to 265 mV. This study presents a strategy utilizing tetracycline-degrading bacteria as bioanodes for TC removal, while incorporating electrogenic bacteria to enhance electricity generation.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Yunhui Tang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Charles Amanze
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Jingxuan Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, Hunan, PR China.
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Li Q, Zheng Y, Guo L, Xiao Y, Li H, Yang P, Xia L, Liu X, Chen Z, Li L, Zhang H. Microbial Degradation of Tetracycline Antibiotics: Mechanisms and Environmental Implications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38835142 DOI: 10.1021/acs.jafc.4c02677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The escalating global consumption of tetracyclines (TCs) as broad-spectrum antibiotics necessitates innovative approaches to mitigate their pervasive environmental persistence and associated risks. While initiatives such as China's antimicrobial reduction efforts highlight the urgency of responsible TC usage, the need for efficient degradation methods remains paramount. Microbial degradation emerges as a promising solution, offering novel insights into degradation pathways and mechanisms. Despite challenges, including the optimization of microbial activity conditions and the risk of antibiotic resistance development, microbial degradation showcases significant innovation in its cost-effectiveness, environmental friendliness, and simplicity of implementation compared to traditional degradation methods. While the published reviews have summarized some aspects of biodegradation of TCs, a systematic and comprehensive summary of all the TC biodegradation pathways, reactions, intermediates, and final products including ring-opening products involved with enzymes and mechanisms of each bacterium and fungus reported is necessary. This review aims to fill the current gap in the literature by offering a thorough and systematic overview of the structure, bioactivity mechanism, detection methods, microbial degradation pathways, and molecular mechanisms of all tetracycline antibiotics in various microorganisms. It comprehensively collects and analyzes data on the microbial degradation pathways, including bacteria and fungi, intermediate and final products, ring-opening products, product toxicity, and the degradation mechanisms for all tetracyclines. Additionally, it points out future directions for the discovery of degradation-related genes/enzymes and microbial resources that can effectively degrade tetracyclines. This review is expected to contribute to advancing knowledge in this field and promoting the development of sustainable remediation strategies for contaminated environments.
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Affiliation(s)
- Qin Li
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
- Collaborative Innovation Center of Hai'xi Green Bio-Manufacturing Technology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
| | - Yanhong Zheng
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
| | - Lijun Guo
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
| | - Ying Xiao
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
| | - Haiyue Li
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
| | - Pingping Yang
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
| | - Li Xia
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Collaborative Innovation Center of Hai'xi Green Bio-Manufacturing Technology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
| | - Xiangqing Liu
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
| | - Zhangyan Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Collaborative Innovation Center of Hai'xi Green Bio-Manufacturing Technology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
| | - Li Li
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
- Collaborative Innovation Center of Hai'xi Green Bio-Manufacturing Technology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
| | - Huaidong Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, People's Republic of China
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
- Collaborative Innovation Center of Hai'xi Green Bio-Manufacturing Technology, Ministry of Education, Fuzhou, Fujian 350117, People's Republic of China
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Yang M, Ma Y, Song X, Miao J, Yan L. Integrative chemical and multiomics analyses of tetracycline removal mechanisms in Pseudomonas sp. DX-21. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134123. [PMID: 38554508 DOI: 10.1016/j.jhazmat.2024.134123] [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: 12/17/2023] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/01/2024]
Abstract
Tetracycline (TC), widely found in various environments, poses significant risks to ecosystems and human health. While efficient biodegradation removes TC, the mechanisms underlying this process have not been elucidated. This study investigated the molecular mechanisms underlying TC biosorption and transfer within the extracellular polymeric substances (EPS) of strain DX-21 and its biodegradation process using fourier transform infrared spectroscopy, molecular docking, and multiomics. Under TC stress, DX-21 increased TC biosorption by secreting more extracellular polysaccharides and proteins, particularly the latter, mitigating toxicity. Moreover, specialized transporter proteins with increased binding capacity facilitated TC movement from the EPS to the cell membrane and within the cell. Transcriptomic and untargeted metabolomic analyses revealed that the presence of TC led to the differential expression of 306 genes and significant alterations in 37 metabolites. Notably, genes related to key enzymes, such as electron transport, peroxidase, and oxidoreductase, exhibited significant differential expression. DX-21 combated and degraded TC by regulating metabolism, altering cell membrane permeability, enhancing oxidative defense, and enhancing energy availability. Furthermore, integrative omics analyses indicated that DX-21 degrades TC via various enzymes, reallocating resources from other biosynthetic pathways. These results advance the understanding of the metabolic responses and regulatory mechanisms of DX-21 in response to TC.
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Affiliation(s)
- Mengya Yang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yifei Ma
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xu Song
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jingwen Miao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lilong Yan
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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Wang S, Han J, Ge Z, Su X, Chen Y, Meng J. Biotransformation characteristics of tetracycline by strain Serratia marcescens MSM2304 and its mechanism evaluation based on products analysis and genomics. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120684. [PMID: 38531133 DOI: 10.1016/j.jenvman.2024.120684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
Microbial biotransformation is a recommended and reliable method in face of formidable tetracycline (TC) with broad-spectrum antibacterial activity. Herein, comprehensive characteristics of a newfound strain and its molecular mechanism in process of TC bioremediation were involved in this study. Specifically, Serratia marcescens MSM2304 isolated from pig manure sludge grew well in presence of TC and achieved optimal removal efficiency of 61% under conditions of initial TC concentration of 10 mg/L, pH of 7.0, cell inoculation amount of 5%, and tryptone of 10 g/L as additional carbon. The pathways of biotransformation include EPS biosorption, cell surface biosorption and biodegradation, which enzymatic processes of biodegradation were occurred through TC adsorbed by biofilms was firstly broken down by extracellular enzymes and part of TC migrated towards biofilm interior and degraded by intracellular enzymes. Wherein extracellular polysaccharides in extracellular polymeric substances (EPS) from biofilm of strain MSM2304 mainly performed extracellular adsorption, and changes in position and intensity of CO, =CH and C-O-C/C-O of EPS possible further implied TC adsorption by it. Biodegradation accounting for 79.07% played a key role in TC biotransformation and could be fitted well by first-order model that manifesting rapid and thorough removal. Potential biodegradation pathway including demethylation, dihydroxylation, oxygenation, and ring opening possibly involved in TC disposal process of MSM2304, TC-degrading metabolites exhibited lower toxicity to indicator bacteria relative to parent TC. Whole genome sequencing as underlying molecular evidence revealed that TC resistance genes, dehydrogenases-encoding genes, monooxygenase-encoding genes, and methyltransferase-encoding genes of strain MSM2304 were positively related to TC biodegradation. Collectively, these results favored a theoretical evaluation for Serratia marcescens MSM2304 as a promising TC-control agent in environmental bioremediation processes.
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Affiliation(s)
- Siyu Wang
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Jie Han
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang,110866, China.
| | - Ziyi Ge
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Xu Su
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Yixuan Chen
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China
| | - Jun Meng
- National Biochar Institute of Shenyang Agricultural University, Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Afairs, 120 # Dongling Road, Shenyang 110866, China.
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Yang M, Jiao Y, Sun L, Miao J, Song X, Yin M, Yan L, Sun N. The performance and mechanism of tetracycline and ammonium removal by Pseudomonas sp. DX-21. BIORESOURCE TECHNOLOGY 2023; 386:129484. [PMID: 37442397 DOI: 10.1016/j.biortech.2023.129484] [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: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
To remove ammonium and tetracycline (TC) from wastewater, a new strain, DX-21, was isolated and exhibited simultaneous removal ability. The performance of DX-21 in TC removal, its removal mechanism, and the potential toxicities of the degradation products were investigated with genomics, mass spectrometry, density functional theory calculations, quantitative structure-activity relationship analyses, and Escherichia coli exposure experiments. DX-21 exhibited removal of ammonium (9.64 mg·L-1·h-1) via assimilation, and TC removal (0.85 mg·L-1·h-1) primarily occurred through cell surface bio-adsorption and biodegradation. Among the 12 identified degradation products, the majority exhibited lower toxicities than TC. Moreover, potential degradation pathways were proposed, including hydroxylation and deamination. Furthermore, DX-21 possessed TC resistance genes, various oxygenases and peroxidases that could potentially contribute to TC degradation. DX-21 colonized activated sludge and significantly enhanced the biodegradation of TC. Therefore, DX-21 showed potential for treating wastewater containing both ammonium and TC.
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Affiliation(s)
- Mengya Yang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Jiao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Luoting Sun
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jingwen Miao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xu Song
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mingyue Yin
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lilong Yan
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
| | - Nan Sun
- College of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin 150030, China
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Aghapour AA, Alizadeh N, Khorsandi H. Biological degradation and mineralization of tetracycline antibiotic using SBR equipped with a vertical axially rotating biological bed (SBR-VARB). Biodegradation 2023; 34:325-340. [PMID: 36840888 PMCID: PMC10191986 DOI: 10.1007/s10532-023-10018-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023]
Abstract
Tetracycline (TC) is a widely used antibiotic with a complex aromatic chemical structure and is highly resistant to biodegradation. In this study, an SBR equipped with a vertical axially rotating biological bed (SBR-VARB) was used for the biodegradation and mineralization of TC. SBR-VARB showed high efficiency in removing TC (97%), total phenolic compounds (TP) (95%), and COD (85%) under optimal operating conditions (TC = 50 mg/L, HRT = 1.75 d, and OLR = 36 g COD/m3 d). The SBR-VARB was able to treat higher concentrations of TC in shorter HRT than reported in previous studies. The contribution of VARB to improve SBR efficiency in removing TC, TP, and COD was 16, 36, and 48%, respectively. Intermediate compounds formed during the biodegradation of TC were identified using GC-MS under the optimal operating conditions of the bioreactor. These are mainly organic compounds with linear chemical structures. Based on the complete biodegradation of TC under the optimal operating conditions of the bioreactor, 93% and 36% of the chlorine and nitrogen atoms in the chemical structure of TC appeared in the wastewater, respectively. According to the sequence analysis of 16SrDNA, Pseudomonas sp., Kocuria Polaris, and Staphylococcus sp. were identified in the biofilm of VARB and the suspended biomass of the bioreactor. Therefore, SBR-VARB showed high efficiency in the biodegradation and mineralization of TC and can be used as a suitable option for treating wastewater containing antibiotics and other toxic compounds.
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Affiliation(s)
- Ali Ahmad Aghapour
- Department of Environmental Health Engineering, Urmia University of Medical Sciences, Urmia, Iran.
| | - Nazila Alizadeh
- Department of Environmental Health Engineering, Urmia University of Medical Sciences, Urmia, Iran
| | - Hassan Khorsandi
- Department of Environmental Health Engineering, Urmia University of Medical Sciences, Urmia, Iran
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Pang S, Lin Z, Chen WJ, Chen SF, Huang Y, Lei Q, Bhatt P, Mishra S, Chen S, Wang H. High-efficiency degradation of methomyl by the novel bacterial consortium MF0904: Performance, structural analysis, metabolic pathways, and environmental bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131287. [PMID: 37003005 DOI: 10.1016/j.jhazmat.2023.131287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several bacterial isolates have been investigated for removing methomyl from environment. However, low degradation efficiency and poor environmental adaptability of pure cultures severely limits their potential for bioremediation of methomyl-contaminated environment. Here, a novel microbial consortium, MF0904, can degrade 100% of 25 mg/L methomyl within 96 h, an efficiency higher than that of any other consortia or pure microbes reported so far. The sequencing analysis revealed that Pandoraea, Stenotrophomonas and Paracoccus were the predominant members of MF0904 in the degradation process, suggesting that these genera might play pivotal roles in methomyl biodegradation. Moreover, five new metabolites including ethanamine, 1,2-dimethyldisulfane, 2-hydroxyacetonitrile, N-hydroxyacetamide, and acetaldehyde were identified using gas chromatography-mass spectrometry, indicating that methomyl could be degraded firstly by hydrolysis of its ester bond, followed by cleavage of the C-S ring and subsequent metabolism. Furthermore, MF0904 can successfully colonize and substantially enhance methomyl degradation in different soils, with complete degradation of 25 mg/L methomyl within 96 and 72 h in sterile and nonsterile soil, respectively. Together, the discovery of microbial consortium MF0904 fills a gap in the synergistic metabolism of methomyl at the community level and provides a potential candidate for bioremediation applications.
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Affiliation(s)
- Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqiu Lin
- The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Shao-Fang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette 47906, USA
| | - Sandhya Mishra
- Environmental Technologies Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
| | - Huishan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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Chen X, Ke Y, Zhu Y, Xu M, Chen C, Xie S. Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130984. [PMID: 36860056 DOI: 10.1016/j.jhazmat.2023.130984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Mingbang Xu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Chao Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, 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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10
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Kim E, Jung HI, Park SH, Kim HY, Kim SK. Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine. AMB Express 2023; 13:30. [PMID: 36899131 PMCID: PMC10006387 DOI: 10.1186/s13568-023-01537-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
The Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8832 coding genes, a core genome of 5452 genes, the accessory genome of 2128 genes, and a unique genome of 1252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside. Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Hae-In Jung
- Department of Animal Sciences and Technology, Konkuk University, Seoul, 05029, Korea
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, 97331, USA
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Korea.
| | - Soo-Ki Kim
- Department of Animal Sciences and Technology, Konkuk University, Seoul, 05029, Korea.
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11
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Zhou D, Liang M, Xia Y, Li C, Huang M, Peng S, Huang Y. Reduction mechanisms of V 5+ by vanadium-reducing bacteria in aqueous environments: Role of different molecular weight fractionated extracellular polymeric substances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158394. [PMID: 36058324 DOI: 10.1016/j.scitotenv.2022.158394] [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: 06/28/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Extracellular polymeric substances (EPS) are high-molecular polymers secreted by microbes and play essential roles in metallic biogeochemical cycling. Previous studies demonstrated the reducing capacity of the functional groups on EPS for metal reduction. However, the roles of different EPS components in vanadium speciation and their responsible reducing substances for vanadium reduction are still unknown. In this study, the EPS of Bacillus sp. PFYN01 was fractionated via ultrafiltration into six components with different kDa (EPS>100, EPS100-50, EPS50-30, EPS30-10, EPS10-3, and EPS<3). Batch reduction experiments of the intact cells, EPS-free cells, the pristine and fractionated EPS with V5+ were conducted and characterized. The results demonstrated that the extracellular reduction of V5+ into V4+ by EPS was the major reduction process. Among the functional groups in EPS, C=O/C-N of amide in protein/polypeptide and CO of carboxyl in fulvic acid-like substances might act as the reductants for V5+, while CO in polysaccharide molecules and PO in phosphodiester played a key role in the adsorption process. The intracellular reduction was via translocating V5+ into the cells and releasing V4+ by the intracellular reductases. The reducing capacity of the fractionated EPS followed a sequence of EPS<3 > EPS10-3 > EPS50-30 > EPS100-50 > EPS30-10 > EPS>100. The small molecules of fulvic acid-like substances and amino acids were responsible for the high reducing capacity of EPS<3. EPS>100 had the lowest reducing capacity due to its macromolecular structure decreasing the exposure of the reactive sites. In addition to reduction, those intermediate EPS components may also have supporting functions, such as connecting protein skeletons and increasing the specific surface area of EPS. Therefore, the diverse effects of the EPS components cannot be neglected in vanadium biogeochemical cycling.
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Affiliation(s)
- Dan Zhou
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China
| | - Mengmeng Liang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Yonglian Xia
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Chao Li
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Mingzheng Huang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Shuming Peng
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China
| | - Yi Huang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, College of Ecology and Environment, Chengdu University of Technology, Sichuan 610059, China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu 610059, China.
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12
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Yang M, Yin M, Zheng Y, Jiang J, Wang C, Liu S, Yan L. Performance and mechanism of tetracycline removal by the aerobic nitrate-reducing strain Pseudomonas sp. XS-18 with auto-aggregation. BIORESOURCE TECHNOLOGY 2022; 359:127442. [PMID: 35688313 DOI: 10.1016/j.biortech.2022.127442] [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: 05/11/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
The coexistence of multiple pollutants has become a distinctive feature of water pollution. However, there are a few strains that can remove nitrate and tetracycline (TC). Here, the efficiency of strain XS-18 in removing nitrate and TC was analyzed, and the mechanism of tolerance and removal of TC was investigated by infrared spectroscopy, three-dimensional fluorescence spectroscopy, and genome analysis. XS-18 could efficiently remove TC (0.40 mg·L-1·h-1) at pH 7.0-11.0 with auto-aggregation. TC was removed via extracellular polymeric substance (EPS) (55.90%) and cell surface (44.10%) adsorption. TC (10 mg/L) could stimulate XS-18 to secrete more polysaccharides and hydrophobic proteins to improve its auto-aggregation ability. The findings also confirmed that TC resistance genes were present. Furthermore, the bacterial flagellum, signal transduction of the chemotactic system and regulatory genes were shown to be related to the auto-aggregation of the strain. XS-18 has potential applications in the treatment of wastewater containing nitrate and TC.
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Affiliation(s)
- Mengya Yang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mingyue Yin
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yaoqi Zheng
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jishuang Jiang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Caixu Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Liu
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lilong Yan
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China.
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13
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Chen X, Shen W, Chen J, Zhu Y, Chen C, Xie S. Tetracycline biotransformation by a novel bacterial strain Alcaligenes sp. T17. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155130. [PMID: 35405229 DOI: 10.1016/j.scitotenv.2022.155130] [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: 02/21/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Comprehensive knowledge on the biotransformation of tetracycline (TC) is critical for the improvement of TC removal in the bioremediation process. This work isolated a novel TC-degrading bacterial strain Alcaligenes sp. T17 and explored its degradation ability under different conditions. Temperature and pH could affect the degradation efficiency, and higher temperature as well as neutral and weakly acidic conditions were conducive to the biotransformation. Response surface methodology predicted the maximum degradation rate of TC (94.35%) under the condition of 25.15 mg/L TC, pH 7.23, and inoculation dosage 1.17% at 40 °C. According to the result of disk diffusion tests, the biodegradation products had lower antimicrobial potency than the parent compound. Five potential biodegradation products were identified, and a possible degradation pathway (degrouping, oxidation and ring-opening) was proposed. The draft genome of strain T17 was also determined. Genomic analysis indicated that strain T17 harbored multiple genes that participated in the metabolism of aromatic compounds as well as genes encoding oxygenases. These functional genes may be relevant to TC biotransformation. This study could provide new insights towards the biotransformation of TC mediated by bacteria.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Wei Shen
- China Waterborne Transport Research Institute, Ministry of Transport of the People's Republic of China, Beijing 100088, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Chao Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, 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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14
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Zhang S, Wang J. Biodegradation of chlortetracycline by Bacillus cereus LZ01: Performance, degradative pathway and possible genes involved. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128941. [PMID: 35462123 DOI: 10.1016/j.jhazmat.2022.128941] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Microbial degradation of chlortetracycline (CTC) is an effective bioremediation method. In the present study, an enrichment technique was used to isolate a Bacillus cereus LZ01 strain capable of effectively degrading CTC from cattle manure. Response surface methodology was used to identify optimized conditions under which strain LZ01 was able to achieve maximal CTC removal (83.58%): temperature of 35.77 °C, solution pH of 7.59, CTC concentration of 57.72 mg/L and microbial inoculum of 0.98%. The antibacterial effect of CTC degradation products on Escherichia coli was investigated by the disk diffusion test, revealing that the products by LZ01 degradation of CTC exhibited lower toxicity than parent compound. Shake flask batch experiments showed that the biodegradation of CTC was a synergistic effect of intracellular and extracellular enzymes, and intracellular enzyme had a better degradation effect on CTC (77.56%). Whole genome sequencing revealed that genes associated with ring-opening hydrolysis, demethylation, deamination and dehydrogenation in strain LZ01 may be involved in the biodegradation of CTC. Subsequent seven possible biodegradation products were identified by LC-MS analyses, and the biodegradation pathways were proposed. Overall, this study provides a theoretical foundation for the characterization and mechanism of CTC degradation in the environment by Bacillus cereus LZ01.
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Affiliation(s)
- Sinan Zhang
- Key Laboratory of Straw Biology and Utilization, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; College of Resource and Environment, Jilin Agricultural University, Changchun 130118, China
| | - Jihong Wang
- College of Resource and Environment, Jilin Agricultural University, Changchun 130118, China.
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15
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Chen X, Yang Y, Ke Y, Chen C, Xie S. A comprehensive review on biodegradation of tetracyclines: Current research progress and prospect. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152852. [PMID: 34995606 DOI: 10.1016/j.scitotenv.2021.152852] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/12/2023]
Abstract
The release of tetracyclines (TCs) in the environment is of significant concern because the residual antibiotics may promote resistance in pathogenic microorganisms, and the transfer of antibiotic resistance genes poses a potential threat to ecosystems. Microbial biodegradation plays an important role in removing TCs in both natural and artificial systems. After long-term acclimation, microorganisms that can tolerate and degrade TCs are retained to achieve efficient removal of TCs under the optimum conditions (e.g. optimal operational parameters and moderate concentrations of TCs). To date, cultivation-based techniques have been used to isolate bacteria or fungi with potential degradation ability. Moreover, the biodegradation mechanism of TCs can be unveiled with the development of chemical analysis (e.g. UPLC-Q-TOF mass spectrometer) and molecular biology techniques (e.g. 16S rRNA gene sequencing, multi-omics sequencing, and whole genome sequencing). In this review, we made an overview of the biodegradation of TCs in different systems, refined functional microbial communities and pure isolates relevant to TCs biodegradation, and summarized the biodegradation products, pathways, and degradation genes of TCs. In addition, ecological risks of TCs biodegradation were considered from the perspectives of metabolic products toxicity and resistance genes. Overall, this article aimed to outline the research progress of TCs biodegradation and propose future research prospects.
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Affiliation(s)
- Xiuli Chen
- 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
| | - Chao Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, 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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16
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He T, Bao J, Leng Y, Kong S, Du J, Li X. Rice straw particles covered with Brevundimonas naejangsanensis DD1 cells can synergistically remove doxycycline from water using adsorption and biotransformation. CHEMOSPHERE 2022; 291:132828. [PMID: 34762878 DOI: 10.1016/j.chemosphere.2021.132828] [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: 08/22/2021] [Revised: 11/03/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Doxycycline (DC) is a second generation tetracycline antibiotic and its occurrence in the aquatic environment due to the discharge of municipal and agricultural wastes has called for technologies to effectively remove DC from water. The objective of the study was to characterize the synergistic benefits of adsorption and biotransformation in removing DC from water using rice straw particles (RSPs) covered with DC degrading bacteria, Brevundimonas naejangsanensis strain DD1. First, optimal experimental conditions were identified for individual processes, i.e., hydrolysis, adsorption, and biotransformation, in terms of their performance of removing DC from water. Then, synergistic effects between adsorption and biotransformation were demonstrated by adding DD1-covered RSPs (DD1-RSPs) to DC-containing solution. Results suggest that DC was quickly adsorbed onto RSPs and the adsorbed DC was subsequently biotransformed by the DD1 cells on RSPs. The adsorption of DC to DD1-RSPs can be well described using the pseudo-second-order kinetics and the Langmuir isotherm. The DD1 cells on RSPs converted DC to several biotransformation products through a series of demethylation, dehydration, decarbonylation, and deamination. This study demonstrated that adsorption and biotransformation could work synergistically to remove DC from water.
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Affiliation(s)
- Ting He
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, PR China; Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA; Institute of Chemistry, Henan Academy of Sciences, Zheng Zhou, Henan Province, 450002, PR China
| | - Jianguo Bao
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, PR China.
| | - Yifei Leng
- School of Civil Engineering, Architecture and Environmental, Hubei University of Technology, Wuhan, 430068, PR China
| | - Shuqiong Kong
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Jiangkun Du
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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17
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Luo J, Xu Y, Wang J, Zhang L, Jiang X, Shen J. Coupled biodegradation of p-nitrophenol and p-aminophenol in bioelectrochemical system: Mechanism and microbial functional diversity. J Environ Sci (China) 2021; 108:134-144. [PMID: 34465427 DOI: 10.1016/j.jes.2021.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 06/13/2023]
Abstract
Biodegradation mechanisms and microbial functional diversity during coupled p-nitrophenol (PNP) and p-aminophenol (PAP) degradation were studied in a bioelectrochemical system. PNP in the biocathode and PAP in the bioanode were almost completely removed within 28hr and 68hr respectively. The degradation followed the steps including hydrating hydroxyalkylation, dehydrogenating carbonylation, and hydrolating ring cleavage, etc. Metagemomic analysis based on the KEGG and eggNOG database annotations revealed the microbial composition and functional genes/enzymes related to phenol degradation in the system. The predominant bacteria genera were Lautropia, Pandoraea, Thiobacillus, Ignavibacterium, Truepera and Hyphomicrobium. The recognized biodegradation genes/enzymes related to pollutant degradation were as follows: pmo, hbd, & ppo for phenol degradation, nzba, amie, & badh for aromatic degradation, and CYP & p450 for xenobiotics degradation, etc. The co-occurrence of ARGs (antibiotic resistant genes), such as adeF, MexJ, ErmF, PDC-93 and Escherichia_coli_mdfA, etc., were annotated in CARD database during the biodegradation process. The Proteobacteria & Actinobacteria phylum was the primary host of both the biodegradation genes & ARGs in this system. The microbial functional diversity ensured the effective biodegradation of the phenol pollutants in the bioelectrochemical system.
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Affiliation(s)
- Jianjun Luo
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuxi Xu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jing Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Libin Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xinbai Jiang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jinyou Shen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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18
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Tan Z, Chen J, Liu Y, Chen L, Xu Y, Zou Y, Li Y, Gong B. The survival and removal mechanism of Sphingobacterium changzhouense TC931 under tetracycline stress and its' ecological safety after application. BIORESOURCE TECHNOLOGY 2021; 333:125067. [PMID: 33878498 DOI: 10.1016/j.biortech.2021.125067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Sphingobacterium changzhouense TC931 was isolated as a novel TC (tetracycline) removal bacterium through adsorption on extracellular polymerase substances (EPS) and cellular surface and biodegradation. TC biodegradation efficiency by strain TC931 was affected by solution initial pH and carbon source. Polysaccharides and hydrocarbons in EPS and cellular surface were responsible for TC biosorption. Eight possible biodegradation products were identified and the biodegradation pathway was proposed. Strain TC931 was rich in antibiotic resistance genes, and tetX-TC931 and antibiotics resistance genome island (GI) may be acquired via horizontal gene transfer in early evolutionary history. The GI was incomplete and may stable in strain TC931, but it could develop into an intact and transferability GI with help of other mobile genetic elements. This work offers a theoretical basis for understanding the survival and biodegradation mechanisms of S. changzhouense TC931 under TC stress, and offers an ecological safety assessment for its application in environmental bioremediation.
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Affiliation(s)
- Zewen Tan
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Jiacheng Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yiling Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Lian Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yuqing Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yixuan Zou
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Beini Gong
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
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19
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Peng T, Liao W, Wang J, Miao J, Peng Y, Gu G, Wu X, Qiu G, Zeng W. Bioleaching and Electrochemical Behavior of Chalcopyrite by a Mixed Culture at Low Temperature. Front Microbiol 2021; 12:663757. [PMID: 34040597 PMCID: PMC8141852 DOI: 10.3389/fmicb.2021.663757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Low-temperature biohydrometallurgy is implicated in metal recovery in alpine mining areas, but bioleaching using microbial consortia at temperatures <10°C was scarcely discussed. To this end, a mixed culture was used for chalcopyrite bioleaching at 6°C. The mixed culture resulted in a higher copper leaching rate than the pure culture of Acidithiobacillus ferrivorans strain YL15. High-throughput sequencing technology showed that Acidithiobacillus spp. and Sulfobacillus spp. were the mixed culture's major lineages. Cyclic voltammograms, potentiodynamic polarization and electrochemical impedance spectroscopy unveiled that the mixed culture enhanced the dissolution reactions, decreased the corrosion potential and increased the corrosion current, and lowered the charge transfer resistance and passivation layer impedance of the chalcopyrite electrode compared with the pure culture. This study revealed the mechanisms via which the mixed culture promoted the chalcopyrite bioleaching.
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Affiliation(s)
- Tangjian Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Wanqing Liao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jingshu Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jie Miao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yuping Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guohua Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
- CSIRO Process Science and Engineering, Clayton, VIC, Australia
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20
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Bottagisio M, Barbacini P, Bidossi A, Torretta E, deLancey-Pulcini E, Gelfi C, James GA, Lovati AB, Capitanio D. Phenotypic Modulation of Biofilm Formation in a Staphylococcus epidermidis Orthopedic Clinical Isolate Grown Under Different Mechanical Stimuli: Contribution From a Combined Proteomic Study. Front Microbiol 2020; 11:565914. [PMID: 33013797 PMCID: PMC7505995 DOI: 10.3389/fmicb.2020.565914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
One of the major causes of prosthetic joint failure is infection. Recently, coagulase negative Staphylococcus epidermidis has been identified as an emergent, nosocomial pathogen involved in subclinical prosthetic joint infections (PJIs). The diagnosis of PJIs mediated by S. epidermidis is usually complex and difficult due to the absence of acute clinical signs derived from the host immune system response. Therefore, analysis of protein patterns in biofilm-producing S. epidermidis allows for the examination of the molecular basis of biofilm formation. Thus, in the present study, the proteome of a clinical isolate S. epidermidis was analyzed when cultured in its planktonic or sessile form to examine protein expression changes depending on culture conditions. After 24 h of culture, sessile bacteria exhibited increased gene expression for ribosomal activity and for production of proteins related to the initial attachment phase, involved in the capsular polysaccharide/adhesin, surface associated proteins and peptidoglycan biosynthesis. Likewise, planktonic S. epidermidis was able to aggregate after 24 h, synthesizing the accumulation associate protein and cell-wall molecules through the activation of the YycFG and ArlRS, two component regulatory pathways. Prolonged culture under vigorous agitation generated a stressful growing environment triggering aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. Further studies will be essential to support these findings in order to further delineate the complex mechanisms of biofilm formation of S. epidermidis and they could provide the groundwork for the development of new drugs against biofilm-related infections, as well as the identification of novel biomarkers of subclinical or chronic infections mediated by these emerging, low virulence pathogens.
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Affiliation(s)
- Marta Bottagisio
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | - Pietro Barbacini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Alessandro Bidossi
- IRCCS Istituto Ortopedico Galeazzi, Laboratory of Clinical Chemistry and Microbiology, Milan, Italy
| | | | - Elinor deLancey-Pulcini
- Medical Biofilm Laboratory, Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Garth A James
- Medical Biofilm Laboratory, Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Arianna B Lovati
- IRCCS Istituto Ortopedico Galeazzi, Cell and Tissue Engineering Laboratory, Milan, Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
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Wu X, Wu X, Zhou X, Gu Y, Zhou H, Shen L, Zeng W. The roles of extracellular polymeric substances of Pandoraea sp. XY-2 in the removal of tetracycline. Bioprocess Biosyst Eng 2020; 43:1951-1960. [PMID: 32500436 DOI: 10.1007/s00449-020-02384-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/25/2020] [Indexed: 11/30/2022]
Abstract
In this study, the roles of extracellular polymeric substances (EPSs) excreted by Pandoraea sp. XY-2 in the removal of tetracycline (TC) were investigated. In the early stage, TC in the solution was mainly removed by the adsorption of EPSs, which accounted for 20% of TC. Thereafter, large amount of TC was transported into the intracellular and biodegraded. EPSs was extracted and the contents of polyprotein and polysaccharides reached their maximum values (30.84 mg/g and 11.15 mg/g) in the first four days. Fourier transform infrared spectroscopy analysis revealed that hydroxyl, methylidyne, methylene and amide I groups in EPSs participated in the adsorption of TC. Furthermore, three-dimensional excitation-emission matrix fluorescence spectroscopy analysis revealed that TC caused the quenching of EPSs fluorescent groups. The quenching mechanism was attributed to static quenching and protein-like substances in EPSs from Pandoraea sp. XY-2 dominated the TC adsorption process. Bioinformatic analysis of Pandoraea sp. XY-2 genome identified multiple genes involved in exopolysaccharide synthesis and EPSs formation. The insights gained in this study might provide a better understanding about the adsorption process of EPSs in tetracycline-contaminated environment.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
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22
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Wu X, Zhou H, Li L, Wang E, Zhou X, Gu Y, Wu X, Shen L, Zeng W. Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. Microorganisms 2020; 8:microorganisms8050716. [PMID: 32408484 PMCID: PMC7284689 DOI: 10.3390/microorganisms8050716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 11/26/2022] Open
Abstract
Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Enhui Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (H.Z.); (L.L.); (E.W.); (X.Z.); (Y.G.); (X.W.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-0731-88877472
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23
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Wu X, Gu Y, Wu X, Zhou X, Zhou H, Amanze C, Shen L, Zeng W. Construction of a Tetracycline Degrading Bacterial Consortium and Its Application Evaluation in Laboratory-Scale Soil Remediation. Microorganisms 2020; 8:microorganisms8020292. [PMID: 32093355 PMCID: PMC7074960 DOI: 10.3390/microorganisms8020292] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC contamination. Microbial remediation, which involves the use of microbes to biodegrade the pollutant, is considered cost-efficient and more suitable for practical application in soil. This study isolated several strains from TC-contaminated soil and constructed a TC-degrading bacterial consortium containing Raoultella sp. XY-1 and Pandoraea sp. XY-2, which exhibited better growth and improved TC degradation efficiency compared with single strain (81.72% TC was biodegraded within 12 days in Lysogeny broth (LB) medium). Subsequently, lab-scale soil remediation was conducted to evaluate its effectiveness in different soils and the environmental effects it brought. Results indicated that the most efficient TC degradation was recorded at 30 °C and in soil sample Y which had relatively low initial TC concentration (around 35 mg/kg): TC concentration decreased by 43.72% within 65 days. Soil properties were affected, for instance, at 30 °C, the pH value of soil sample Y increased to near neutral, and soil moisture content (SMC) of both soils declined. Analysis of bacterial communities at the phylum level showed that Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi were the four dominant phyla, and the relative abundance of Proteobacteria significantly increased in both soils after bioremediation. Further analysis of bacterial communities at the genus level revealed that Raoultella sp. XY-1 successfully proliferated in soil, while Pandoraea sp. XY-2 was undetectable. Moreover, bacteria associated with nitrogen cycling, biodegradation of organic pollutants, soil biochemical reactions, and plant growth were affected, causing the decline in soil bacterial diversity. Variations in the relative abundance of tetracycline resistance genes (TRGs) and mobile gene elements (MGEs) were investigated, the results obtained indicated that tetD, tetG, tetX,intI1, tnpA-04, and tnpA-05 had higher relative abundance in original soils, and the relative abundance of most TRGs and MGEs declined after the microbial remediation. Network analysis indicated that tnpA may dominate the transfer of TRGs, and Massilia, Alkanibacter, Rhizomicrobium, Xanthomonadales, Acidobacteriaceae, and Xanthomonadaceae were possible hosts of TRGs or MGEs. This study comprehensively evaluated the effectiveness and the ecological effects of the TC-degrading bacterial consortium in soil environment.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Yichao Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
| | - Xiangyu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
| | - Han Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
| | - Charles Amanze
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (X.W.); (Y.G.); (X.W.); (X.Z.); (H.Z.); (C.A.); (L.S.)
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
- Correspondence: ; Tel.: +86-0731-88877472
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24
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Peeters C, De Canck E, Cnockaert M, De Brandt E, Snauwaert C, Verheyde B, Depoorter E, Spilker T, LiPuma JJ, Vandamme P. Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism. Front Microbiol 2019; 10:2556. [PMID: 31781066 PMCID: PMC6851202 DOI: 10.3389/fmicb.2019.02556] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 01/31/2023] Open
Abstract
Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available Pandoraea genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA–DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea has an open pan genome that includes many orthogroups in the ‘Xenobiotics biodegradation and metabolism’ KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).
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Affiliation(s)
- Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evie De Brandt
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Bart Verheyde
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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25
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Role of extracellular polymeric substance (EPS) in toxicity response of soil bacteria Bacillus sp. S3 to multiple heavy metals. Bioprocess Biosyst Eng 2019; 43:153-167. [PMID: 31549306 DOI: 10.1007/s00449-019-02213-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/20/2019] [Accepted: 09/10/2019] [Indexed: 10/25/2022]
Abstract
Heavy metal resistant bacteria are of great interest because of their potential use in bioremediation. Understanding the survival and adaptive strategies of these bacteria under heavy metal stress is important for better utilization of these bacteria in remediation. The objective of this study was to investigate the role of bacterial extracellular polymeric substance (EPS) in detoxifying against different heavy metals in Bacillus sp. S3, a new hyper antimony-oxidizing bacterium previously isolated from contaminated mine soils. The results showed that Bacillus sp. S3 is a multi-metal resistant bacterial strain, especially to Sb(III), Cu(II) and Cr(VI). Toxic Cd(II), Cr(VI) and Cu(II) could stimulate the secretion of EPS in Bacillus sp. S3, significantly enhancing the adsorption and detoxification capacity of heavy metals. Both Fourier transform infrared spectroscopy (FTIR) and three-dimensional excitation-emission matrix (3D-EEM) analysis further confirmed that proteins were the main compounds of EPS for metal binding. In contrast, the EPS production was not induced under Sb(III) stress. Furthermore, the TEM-EDX micrograph showed that Bacillus sp. S3 strain preferentially transported the Sb(III) to the inside of the cell rather than adsorbed it on the extracellular surface, indicating intracellular detoxification rather than extracellular EPS precipitation played an important role in microbial resistance towards Sb(III). Together, our study suggests that the toxicity response of EPS to heavy metals is associated with difference in EPS properties, metal types and corresponding environmental conditions, which is likely to contribute to microbial-mediated remediation.
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26
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Xia M, Bao P, Zhang S, Liu A, Shen L, Yu R, Liu Y, Chen M, Li J, Wu X, Qiu G, Zeng W. Extraction and characterization of extracellular polymeric substances from a mixed fungal culture during the adaptation process with waste printed circuit boards. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:22137-22146. [PMID: 31209748 DOI: 10.1007/s11356-019-05234-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Extracellular polymeric substances (EPSs) extracted from fungal mycelium by four chemical methods (NaOH, H2SO4, formaldehyde-NaOH, glutaraldehyde-NaOH), three physical methods (heating, ultrasound, vibration), and a control method (centrifugation alone) were investigated. Results indicated formaldehyde-NaOH outperformed other methods with 186.6 ± 8.0 mg/g of polysaccharides and 23.2 ± 4.6 mg/g of protein extracted and ensured little contamination by intracellular substances. Thereafter, this method was applied in extracting EPS from a mixed fungal culture in the adaptation process with 0.5% (w/v) waste printed circuit boards (PCBs). With the four adaptation stages continuing, the culture tended to become more sensitive to respond to the external toxic environment characterized by secreting EPS more easily and quickly. The maximum amount of polysaccharides and protein could be achieved in only 3 days both at the 3rd and 4th adaptation stage. Three-dimensional excitation-emission matrix fluorescence spectrum indicated the peaks obtained for EPS were mainly associated to soluble microbial by-product-like and aromatic protein-like compounds. Transmission electron microscopic observation illustrated that although metal ions penetrated into hypha cells, parts of them could be absorbed by EPS, implying that EPS secretion may be a primary protective strategy adopted by the culture.
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Affiliation(s)
- Mingchen Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Peng Bao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Shishi Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Ajuan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Miao Chen
- CSIRO Process Science and Engineering, Clayton, Victoria, 3168, Australia
- Centre for Advanced Materials and Industrial Chemistry, RMIT University, Melbourne, 3000, Australia
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
- CSIRO Process Science and Engineering, Clayton, Victoria, 3168, Australia.
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27
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Increased chalcopyrite bioleaching capabilities of extremely thermoacidophilic Metallosphaera sedula inocula by mixotrophic propagation. J Ind Microbiol Biotechnol 2019; 46:1113-1127. [PMID: 31165968 DOI: 10.1007/s10295-019-02193-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales, such as Metallosphaera sedula, are metabolically versatile and of great relevance in bioleaching. However, the impacts of extreme thermoacidophiles propagated with different energy substrates on subsequent bioleaching of refractory chalcopyrite remain unknown. Transcriptional responses underlying their different bioleaching potentials are still elusive. Here, it was first showed that M. sedula inocula propagated with typical energy substrates have different chalcopyrite bioleaching capabilities. Inoculum propagated heterotrophically with yeast extract was deficient in bioleaching; however, inoculum propagated mixotrophically with chalcopyrite, pyrite or sulfur recovered 79%, 78% and 62% copper, respectively, in 12 days. Compared with heterotrophically propagated inoculum, 937, 859 and 683 differentially expressed genes (DEGs) were identified in inoculum cultured with chalcopyrite, pyrite or sulfur, respectively, including upregulation of genes involved in bioleaching-associated metabolism, e.g., Fe2+ and sulfur oxidation, CO2 fixation. Inoculum propagated with pyrite or sulfur, respectively, shared 480 and 411 DEGs with chalcopyrite-cultured inoculum. Discrepancies on repertories of DEGs that involved in Fe2+ and sulfur oxidation in inocula greatly affected subsequent chalcopyrite bioleaching rates. Novel genes (e.g., Msed_1156, Msed_0549) probably involved in sulfur oxidation were first identified. This study highlights that mixotrophically propagated extreme thermoacidophiles especially with chalcopyrite should be inoculated into chalcopyrite heaps at industrial scale.
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28
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Zhang X, Liu X, Li L, Wei G, Zhang D, Liang Y, Miao B. Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations. BMC Genomics 2019; 20:438. [PMID: 31146680 PMCID: PMC6543593 DOI: 10.1186/s12864-019-5827-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 01/18/2023] Open
Abstract
Background Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. Results Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation. Conclusions Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5827-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- School of Life Sciences, Nantong University, Nantong, China
| | - Danli Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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29
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Dissolution and Passivation of Chalcopyrite during Bioleaching by Acidithiobacillus ferrivorans at Low Temperature. MINERALS 2019. [DOI: 10.3390/min9060332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Our knowledge on the dissolution and passivation mechanisms of chalcopyrite during bioleaching at low temperature has been limited to date. In this study, an Acidithiobacillus ferrivorans strain with high tolerance to heavy metals and UV radiation was used for chalcopyrite bioleaching. At 6 °C, no apparent precipitate was detected on the mineral surface after bioleaching using a scanning electron microscope (SEM). X-ray diffraction (XRD) revealed that the ore residue contained only chalcopyrite and quartz. X-ray photoelectron spectroscopy (XPS) analysis revealed that the content of S0 on the mineral surface remained low and the ratio of SO42− decreased from 46.7% to 20.9%, but the amount of Sn2− increased from 10.4% to 21.4% after bioleaching. Expression of five critical iron- and sulfur-oxidation genes during bioleaching was analyzed using quantitative real-time PCR. The gene rusA had higher expression in the mid-log phase than in the stationary phase but hdrA and cyoC1 showed an opposite trend. All genes had higher expression at 6 °C than at 28 °C, so as to compensate for the decline in the enzyme activities. The study revealed that polysulfide was the most plausible passivating substance at 6 °C, and the strain can maintain the iron- and sulfur-oxidation activities during low-temperature bioleaching.
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Chen L, Yang S, Wen C, Zheng S, Yang Y, Feng X, Chen J, Luo D, Liu R, Yang F. Regulation of Microcystin-LR-Induced DNA Damage by miR-451a in HL7702 Cells. Toxins (Basel) 2019; 11:toxins11030164. [PMID: 30875960 PMCID: PMC6468842 DOI: 10.3390/toxins11030164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 11/16/2022] Open
Abstract
Microcystin-LR is a cyclic heptapeptide hepatotoxin produced by harmful cyanobacteria. A panel of microRNAs containing miR-451a were found to be significantly changed in normal human liver cells HL7702 after exposure to microcystin-LR (MC-LR) in our previous study. However, the functions of miR-451a in hepatotoxicity induced by MC-LR remained unclear. The study aimed to investigate the impacts of miR-451a in HL7702 cells following treatment with 5 or 10 μM MC-LR. The comet assay indicated that MC-LR can influence Olive tail moment (OTM) in HL7702 cells. Furthermore, increase of miR-451a significantly repressed DNA damage and the protein expression level of γ-H2AX induced by MC-LR. Moreover, over-expression of miR-451a inhibited the expression level of p-AKT1 protein in cells following treatment by MC-LR. These results showed that miR-451a may protect from MC-LR-induced DNA damage by down-regulating the expression of p-AKT1, which provides new clues for the diagnosis and therapy policies for liver damage induced by MC-LR.
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Affiliation(s)
- Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Shu Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Cong Wen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Shuilin Zheng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Yue Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Xiangling Feng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Jihua Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Dan Luo
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing 210007, China.
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410078, China.
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing 210007, China.
- Key laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, China.
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