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Vaziri Y, Asgari G, Ghorbani-Shahna F, Madrakian T, Shokoohi R, Seid-Mohammadi A. Degradation of 2,4-dinitrotoluene in aqueous solution by dielectric barrier discharge plasma combined with Fe-RGO-BiVO 4 nanocomposite. Sci Rep 2024; 14:2480. [PMID: 38291089 PMCID: PMC10827745 DOI: 10.1038/s41598-024-52286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024] Open
Abstract
2,4-Dinitrotoluene (2,4-DNT) as a priority and hazardous pollutant, is widely used in industrial and military activities. In this study the synergistic effect of Fe-RGO-BiVO4 nanocomposite in a non-thermal dielectric barrier discharge plasma reactor (NTP-DBD) for degrading 2,4-DNT was evaluated. Preparation of the Fe-RGO-BiVO4 nanocomposite was done by a stepwise chemical method depositing Fe and reduced graphene oxide (RGO) on BiVO4. Field emission scanning electron microscopy (FESEM), X-ray diffraction analysis (XRD), UV-vis diffuse reflectance spectra (DRS), and energy-dispersive X-ray spectroscopy mapping (EDS-mapping) validated the satisfactory synthesis of Fe-RGO-BiVO4. To find the optimal conditions and to determine the interaction of model parameters, a central composite design (RSM-CCD) had been employed. 2,4 DNT can be completely degraded at: initial 2,4-DNT concentration of 40 mg L-1, Fe-RGO-BiVO4 dosage of 0.75 g L-1, applied voltage of 21kV, reaction time of 30 min and pH equal to 7, while the single plasma process reached a degradation efficiency of 67%. The removal efficiency of chemical oxygen demand (COD) and total organic carbon (TOC) were 90.62% and 88.02% at 30 min contact time, respectively. Results also indicated that average oxidation state (AOS) and carbon oxidation state (COS) were enhanced in the catalytic NTP-DBD process, which demonstrate the effectiveness of proposed process for facilitating biodegradability of 2,4-DNT.
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Affiliation(s)
- Yaser Vaziri
- Department of Environmental Health Engineering, Hamadan University of Medical Science, Hamadan, Iran
| | - Ghorban Asgari
- Social Determinants of Health Research Center (SDHRC), Faculty of Public Health, Department of Environmental Health Engineering, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farshid Ghorbani-Shahna
- Center of Excellence for Occupational Health, Occupational Health and Safety Research Center, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Reza Shokoohi
- Department of Environmental Health Engineering, Hamadan University of Medical Science, Hamadan, Iran
| | - Abdolmotaleb Seid-Mohammadi
- Social Determinants of Health Research Center (SDHRC), Faculty of Public Health, Department of Environmental Health Engineering, Hamadan University of Medical Sciences, Hamadan, Iran.
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Wang D, Naqvi STA, Lei F, Zhang Z, Yu H, Ma LZ. Glycosyl hydrolase from Pseudomonas fluorescens inhibits the biofilm formation of Pseudomonads. Biofilm 2023; 6:100155. [PMID: 37928620 PMCID: PMC10622837 DOI: 10.1016/j.bioflm.2023.100155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023] Open
Abstract
Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic counterparts. Novel strategies are required to encounter biofilms. Exopolysaccharides are one of the major components of biofilm matrix and play a vital role in biofilm architecture. In previous studies, a glycosyl hydrolase, PslGPA, from Pseudomonas aeruginosa was found to be able to inhibit biofilm formation by disintegrating exopolysaccharide in biofilms. Here, we investigate the potential spectrum of PslG homologous protein with anti-biofilm activity. One glycosyl hydrolase from Pseudomonas fluorescens, PslGPF, exhibits anti-biofilm activities and the key catalytic residues of PslGPF are conserved with those of PslGPA. PslGPF at concentrations as low as 50 nM efficiently inhibits the biofilm formation of P. aeruginosa and disassemble its preformed biofilm. Furthermore, PslGPF exhibits anti-biofilm activity on a series of Pseudomonads, including P. fluorescens, Pseudomonas stutzeri and Pseudomonas syringae pv. phaseolicola. PslGPF stays active under various temperatures. Our findings suggest that P. fluorescens glycosyl hydrolase PslGPF has potential to be a broad spectrum inhibitor on biofilm formation of a wide range of Pseudomonads.
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Affiliation(s)
- Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Syed Tatheer Alam Naqvi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Fanglin Lei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Yunnan University, Kunming, 650500, PR China
| | - Zhenyu Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
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Gao J, Li Z, Zhu B, Wang L, Xu J, Wang B, Fu X, Han H, Zhang W, Deng Y, Wang Y, Zuo Z, Peng R, Tian Y, Yao Q. Creation of Environmentally Friendly Super "Dinitrotoluene Scavenger" Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303785. [PMID: 37715295 PMCID: PMC10602510 DOI: 10.1002/advs.202303785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Pervasive environmental contamination due to the uncontrolled dispersal of 2,4-dinitrotoluene (2,4-DNT) represents a substantial global health risk, demanding urgent intervention for the removal of this detrimental compound from affected sites and the promotion of ecological restoration. Conventional methodologies, however, are energy-intensive, susceptible to secondary pollution, and may inadvertently increase carbon emissions. In this study, a 2,4-DNT degradation module is designed, assembled, and validated in rice plants. Consequently, the modified rice plants acquire the ability to counteract the phytotoxicity of 2,4-DNT. The most significant finding of this study is that these modified rice plants can completely degrade 2,4-DNT into innocuous substances and subsequently introduce them into the tricarboxylic acid cycle. Further, research reveals that the modified rice plants enable the rapid phytoremediation of 2,4-DNT-contaminated soil. This innovative, eco-friendly phytoremediation approach for dinitrotoluene-contaminated soil and water demonstrates significant potential across diverse regions, substantially contributing to carbon neutrality and sustainable development objectives by repurposing carbon and energy from organic contaminants.
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Zhang WH, Deng YD, Chen ZF, Zuo ZH, Tian YS, Xu J, Wang B, Wang LJ, Han HJ, Li ZJ, Wang Y, Yao QH, Gao JJ, Fu XY, Peng RH. Metabolic engineering of Escherichia coli for 2,4-dinitrotoluene degradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115287. [PMID: 37567105 DOI: 10.1016/j.ecoenv.2023.115287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023]
Abstract
2,4-Dinitrotoluene (2,4-DNT) as a common industrial waste has been massively discharged into the environment with industrial wastewater. Due to its refractory degradation, high toxicity, and bioaccumulation, 2,4-DNT pollution has become increasingly serious. Compared with the currently available physical and chemical methods, in situ bioremediation is considered as an economical and environmentally friendly approach to remove toxic compounds from contaminated environment. In this study, we relocated a complete degradation pathway of 2,4-DNT into Escherichia coli to degrade 2,4-DNT completely. Eight genes from Burkholderia sp. strain were re-synthesized by PCR-based two-step DNA synthesis method and introduced into E. coli. Degradation experiments revealed that the transformant was able to degrade 2,4-DNT completely in 12 h when the 2,4-DNT concentration reached 3 mM. The organic acids in the tricarboxylic acid cycle were detected to prove the degradation of 2,4-DNT through the artificial degradation pathway. The results proved that 2,4-DNT could be completely degraded by the engineered bacteria. In this study, the complete degradation pathway of 2,4-DNT was constructed in E. coli for the first time using synthetic biology techniques. This research provides theoretical and experimental bases for the actual treatment of 2,4-DNT, and lays a technical foundation for the bioremediation of organic pollutants.
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Affiliation(s)
- Wen-Hui Zhang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Yong-Dong Deng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Zhi-Feng Chen
- College of Biology and Agricultural Technology, Zunyi Normal College, Zunyi, China
| | - Zhi-Hao Zuo
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Yong-Sheng Tian
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Jing Xu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Bo Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Li-Juan Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Hong-Juan Han
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Zhen-Jun Li
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Yu Wang
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Quan-Hong Yao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China
| | - Jian-Jie Gao
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China.
| | - Xiao-Yan Fu
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China.
| | - Ri-He Peng
- Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, China; Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China.
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Dhawi F. The Role of Plant Growth-Promoting Microorganisms (PGPMs) and Their Feasibility in Hydroponics and Vertical Farming. Metabolites 2023; 13:metabo13020247. [PMID: 36837866 PMCID: PMC9964210 DOI: 10.3390/metabo13020247] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
There are many reasons for the increase in hydroponics/soil-free systems in agriculture, and these systems have now advanced to the form of vertical farming. The sustainable use of space, the reduction in water use compared to soil-based agriculture, the lack of pesticides, the ability to control nutrient inputs, and the implementation of user-friendly technology for environmental control and harvesting are all factors that have made the global market for vertical farming predicted to reach more than USD 10.02 billion by 2027. By comparison, soil-based agriculture consumes 20 times more water, and some agricultural practices promote soil deterioration and cause environmental pollution. Plant growth-promoting microorganisms (PGPMs) have been used extensively in traditional agriculture to enhance plant growth, environmental stress tolerance, and the efficacy of phytoremediation in soil-based farming. Due to the controlled atmosphere in hydroponics and vertical farms, there is strong potential to maximize the use of PGPMs. Here, we review the leveraging of plant growth-promoting microorganism mechanisms in hydroponics and vertical farming. We recommend a synchronized PGPM treatment using a biostimulant extract added to the hydroponic medium while also pre-treating seeds or seedlings with a microbial suspension for aquaponic and aeroponic systems.
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Affiliation(s)
- Faten Dhawi
- Agricultural Biotechnology Department, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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Wang B, Gao J, Xu J, Fu X, Han H, Li Z, Wang L, Zhang F, Tian Y, Peng R, Yao Q. Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126428. [PMID: 34171665 DOI: 10.1016/j.jhazmat.2021.126428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a 13C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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Yap HS, Zakaria NN, Zulkharnain A, Sabri S, Gomez-Fuentes C, Ahmad SA. Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation. BIOLOGY 2021; 10:biology10050354. [PMID: 33922046 PMCID: PMC8143585 DOI: 10.3390/biology10050354] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions. Abstract The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.
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Affiliation(s)
- How Swen Yap
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.S.Y.); (N.N.Z.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda, Bulnes, Punta Arenas 01855, Chile
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence:
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Zhang B, Sun L, Song X, Huang D, Li M, Peng C, Wang W. Genetically engineered thermotolerant facultative anaerobes for high-efficient degradation of multiple hazardous nitroalkanes. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124253. [PMID: 33144004 DOI: 10.1016/j.jhazmat.2020.124253] [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: 08/05/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Nitroalkanes are important industrial raw materials but also toxic pollutants, which are difficult to degrade once released into the environment. In this study, to significantly improve the degradation-efficiency of multiple nitroalkanes, a facultative anaerobe was genetically engineered, possible influencing factors and simulated application experiments of bioreactor were tested and evaluated. Among all engineered recombinants, the most effective strains NG-S1 (anaerobic) and NG-S2 (aerobic) displayed 2-fold and 2.8-fold final degradation rates higher than the wild type, respectively. Exogenous components, particularly those that enhance coenzyme synthesis, helped to increase the degradation rate, as the level of coenzymes affected full function of overexpressed nitroalkane oxidase. Importantly, simulated mixed-nitroalkane-wastewater bioreactor experiments proved excellent and sustainable degradation performance of the engineered strains for potential industrial applications. Collectively, these findings provide a promising thermophilic biological engineering platform and a new perspective for high-efficient and continuous environmental bioremediation of hazardous pollutants under aerobic and anaerobic conditions.
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Affiliation(s)
- Bingling Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Linbo Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xiaoru Song
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Chenchen Peng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
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9
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Xu X, Xi B, Zhang Y, Xia F, Han X, Gao P, Wan S, Jiang Y, Yang Y. A comparative study on the treatment of 2,4-dinitrotoluene contaminated groundwater in the combined system: efficiencies, intermediates and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139161. [PMID: 32474247 DOI: 10.1016/j.scitotenv.2020.139161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
In this study, scrap irons (SI)/granular activated carbons (GAC) micro-electrolysis treatment and persulfate-releasing materials (PRM) treatment were employed to construct the combination reduction and oxidation system to treat 2,4-dinitrotoluene (2,4-DNT) contaminated groundwater. The 2,4-DNT treatment efficiencies in the PRM pre-treatment before SI/GAC micro-electrolysis treatment (FM-1 = PRM + SI/GAC) and SI/GAC micro-electrolysis pre-treatment before the PRM treatment (FM-3 = SI/GAC + PRM) were investigated in two separated columns. As control groups, the separated SI and GAC instead of the SI/GAC mixture were used in another two separated columns (FM-2 = PRM + SI + GAC; FM-4 = SI + GAC + PRM). The highest treatment efficiencies of 2,4-DNT in the FM-1 and FM-3 systems reached 79% and 93% during 5 PV, respectively. We found that the filling position of SI, GAC and PRM significantly affected the variations of pH, oxidation-reduction potential, Fe2+ and S2O82- concentrations in the combined systems. These results indicated that the SI/GAC micro-electrolysis pre-treatment of 2,4-DNT before the PRM treatment (FM-3) is more beneficial. The fifteen main intermediates in the combined system were identified by the detection of liquid chromatograph mass spectrometer. Furthermore, the possible treatment pathways of 2.4-DNT were proposed on the basis of identified intermediates. The treatment mechanisms in the FM-1 and FM-3 systems were proposed with the reduction mechanism in the SI/GAC micro-electrolysis system and the oxidation mechanism in the PRM treatment. Therefore, the combination of the reduction pre-treatment with the SI/GAC micro-electrolysis system and the oxidation post-treatment with persulfate can effectively treat the nitroaromatic compounds contaminated groundwater.
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Affiliation(s)
- Xiangjian Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Yan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Fu Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Xu Han
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Puchuang Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Shuoyang Wan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Yonghai Jiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Yu Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
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Akkaya Ö. Nicotiana tabacum-associated bioengineered Pseudomonas putida can enhance rhizoremediation of soil containing 2,4-dinitrotoluene. 3 Biotech 2020; 10:398. [PMID: 32864284 PMCID: PMC7438454 DOI: 10.1007/s13205-020-02395-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
Rhizoremediation processes are based on plant-bacteria interactions and can be effectively used for cleaning many pollutants from the environment to overcome the constraints of individual phytoremediation. Here, 1 mM and 1.5 mM concentrations of 2,4-dinitrotoluene (2,4-DNT) degrading Pseudomonas putida (P. putida) strain KT.DNT and various growth stages of Nicotiana tabacum (N. tabacum) were initially assayed in in vitro tissue culture system and the best conditions for the association of plant-rhizobacterium were ascertained to remediation of the soil contaminated with 2,4-DNT. 5-days old N. tabacum plants inoculated with 2 × 106 cfu/mL bacterial inoculum for 3 weeks were preferred for rhizoremediation experiments as they showed a nearly threefold increase in the fresh and dry biomass in comparison to noninoculated ones. When these seedlings were planted either alone or together with P. putida KT2440 or P. putida KT.DNT in soils contaminated with 1 mM and 1.5 mM of 2,4-DNT, the maximum degradation rate of 98% and ~ 93% were determined at the end of 14 days by KT.DNT inoculated tobacco plants. Our results indicate that it would be advantageous to use the 2,4-DNT-degrading bacterium inoculated with N. tabacum plants to accelerate and enhance the cleanup of soil contaminated with 2,4-DNT.
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Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
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11
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Kayıhan DS, Kayıhan C, Özden Çiftçi Y. Transgenic tobacco plants overexpressing a cold-adaptive nitroreductase gene exhibited enhanced 2,4-dinitrotoluene detoxification rate at low temperature. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 23:1-9. [PMID: 32643388 DOI: 10.1080/15226514.2020.1786795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plants encounter many environmental factors such as low and high temperatures during phytoremediation processes. In this study, our aim was to produce the transgenic tobacco plants by using a newly characterized bacterial nitroreductase, Ntr, which was active at a broad range temperature in order to detoxify 2,4-dinitrotoluene (2,4-DNT) at lower temperature. The presence of Ntr and its heterologous expression was verified in T1 transgenic plants and their growing ability were determined under toxic amount of 2,4-DNT (35 µM). Fresh weight and dry weight of transgenic plants were significantly higher than wild type (WT) under toxic 2,4-DNT at 22 °C, indicating higher growth capacity of the transgenics. Transgenic plants also showed a higher tolerance than WT when exposed to 2,4-DNT at 15 °C. Moreover, transformation rate of 2,4-DNT was gradually decreased through decreasing temperatures in WT media, however, it was increased through decreasing temperatures in transgenic plant TR3-25 media and it had the highest transformation rate (54%) of 2,4-DNT at 4 °C. Correlatively, 2,4-DNT treatment at 4 °C led to a significant decrease in H2O2 level in transgenic plants. Thus, transgenic plants overexpressing nitroreductase might have an important advantage for phytoremediation of toxic nitroaromatic compounds in field applications at low temperatures.
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Affiliation(s)
- Doğa Selin Kayıhan
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Ceyhun Kayıhan
- Department of Molecular Biology and Genetics, Başkent University, Ankara, Turkey
| | - Yelda Özden Çiftçi
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
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12
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Fedeson DT, Saake P, Calero P, Nikel PI, Ducat DC. Biotransformation of 2,4-dinitrotoluene in a phototrophic co-culture of engineered Synechococcus elongatus and Pseudomonas putida. Microb Biotechnol 2020; 13:997-1011. [PMID: 32064751 PMCID: PMC7264894 DOI: 10.1111/1751-7915.13544] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/28/2022] Open
Abstract
In contrast to the current paradigm of using microbial mono-cultures in most biotechnological applications, increasing efforts are being directed towards engineering mixed-species consortia to perform functions that are difficult to programme into individual strains. In this work, we developed a synthetic microbial consortium composed of two genetically engineered microbes, a cyanobacterium (Synechococcus elongatus PCC 7942) and a heterotrophic bacterium (Pseudomonas putida EM173). These microbial species specialize in the co-culture: cyanobacteria fix CO2 through photosynthetic metabolism and secrete sufficient carbohydrates to support the growth and active metabolism of P. putida, which has been engineered to consume sucrose and to degrade the environmental pollutant 2,4-dinitrotoluene (2,4-DNT). By encapsulating S. elongatus within a barium-alginate hydrogel, cyanobacterial cells were protected from the toxic effects of 2,4-DNT, enhancing the performance of the co-culture. The synthetic consortium was able to convert 2,4-DNT with light and CO2 as key inputs, and its catalytic performance was stable over time. Furthermore, cycling this synthetic consortium through low nitrogen medium promoted the sucrose-dependent accumulation of polyhydroxyalkanoate, an added-value biopolymer, in the engineered P. putida strain. Altogether, the synthetic consortium displayed the capacity to remediate the industrial pollutant 2,4-DNT while simultaneously synthesizing biopolymers using light and CO2 as the primary inputs.
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Affiliation(s)
- Derek T. Fedeson
- DOE‐MSU Plant Research LaboratoriesMichigan State UniversityEast LansingMIUSA
- Genetics ProgramMichigan State UniversityEast LansingMIUSA
| | - Pia Saake
- Heinrich‐Heine UniversitätDüsseldorfGermany
| | - Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs LyngbyDenmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs LyngbyDenmark
| | - Daniel C. Ducat
- DOE‐MSU Plant Research LaboratoriesMichigan State UniversityEast LansingMIUSA
- Genetics ProgramMichigan State UniversityEast LansingMIUSA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMIUSA
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Okozide OE, Adebusoye SA, Obayori OS. Aerobic degradation of 2,4-dinitrotoluene: Effect of raw organic wastes and nitrogen fortification. JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:835-846. [PMID: 33016493 DOI: 10.1002/jeq2.20088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
2,4-Dinitrotoluene (2,4-DNT), a principal derivative generated in the synthesis of 2,4,6-trinitrotoluene, is widely used as a waterproofer, plasticizer, and gelatinizer in propellants and explosives. This compound has been documented as a priority pollutant because of its toxicity. Therefore, its removal from contaminated systems is a major focus of research and environmental attention. The presence of 2,4-DNT bacterial-degrading strains that could utilize 2,4-DNT as growth substrate in polluted sites in Ibadan, Nigeria, was determined using continual enrichment techniques on nitroaromatic mixtures. Proteus sp. strain OSES2 isolated in this study was characterized by phenotypic typing and 16S ribosomal RNA gene sequencing. Growth of the strain on 2,4-DNT resulted in an exponential increase in biomass and complete substrate utilization within 72 h, accompanied by NO3 - elimination. Degradation competence was enhanced in the presence of corn steep liquor, molasses, and Tween 80 compared with incubation without amendment. Conversely, amendment with nitrogen sources yielded no significant improvement in degradation. Use of these organic wastes as candidates in a bioremediation strategy should be exploited. This would provide a less-expensive organic source supplement for cleanup purposes, with the ultimate aim of reducing the cost of bioremediation while reducing wastes intended for landfill.
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Affiliation(s)
- Osekokhune E Okozide
- Dep. of Microbiology, Faculty of Science, Univ. of Lagos, Akoka, Lagos, 100213, Nigeria
| | - Sunday A Adebusoye
- Dep. of Microbiology, Faculty of Science, Univ. of Lagos, Akoka, Lagos, 100213, Nigeria
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14
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Wendisch VF, Brito LF, Gil Lopez M, Hennig G, Pfeifenschneider J, Sgobba E, Veldmann KH. The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources. J Biotechnol 2016; 234:139-157. [DOI: 10.1016/j.jbiotec.2016.07.022] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
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15
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George KW, Hay AG. Bacterial strategies for growth on aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:1-33. [PMID: 21459192 DOI: 10.1016/b978-0-12-387022-3.00005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the biodegradation of aromatic compounds has been studied for over 40 years, there is still much to learn about the strategies bacteria employ for growth on novel substrates. Elucidation of these strategies is crucial for predicting the environmental fate of aromatic pollutants and will provide a framework for the development of engineered bacteria and degradation pathways. In this chapter, we provide an overview of studies that have advanced our knowledge of bacterial adaptation to aromatic compounds. We have divided these strategies into three broad categories: (1) recruitment of catabolic genes, (2) expression of "repair" or detoxification proteins, and (3) direct alteration of enzymatic properties. Specific examples from the literature are discussed, with an eye toward the molecular mechanisms that underlie each strategy.
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Affiliation(s)
- Kevin W George
- Field of Environmental Toxicology, Cornell University Ithaca, New York, USA; Department of Microbiology, Wing Hall, Cornell University Ithaca, New York, USA
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16
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Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol 2014; 10:731. [PMID: 24952589 PMCID: PMC4265053 DOI: 10.15252/msb.20134955] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs.
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Affiliation(s)
- Iman Farasat
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Jason Collens
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Michael Easterbrook
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Matthew Guido
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Howard M Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
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17
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Liu N, Li H, Ding F, Xiu Z, Liu P, Yu Y. Analysis of biodegradation by-products of nitrobenzene and aniline mixture by a cold-tolerant microbial consortium. JOURNAL OF HAZARDOUS MATERIALS 2013; 260:323-329. [PMID: 23774783 DOI: 10.1016/j.jhazmat.2013.05.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
A cold-tolerant microbial consortium, which can use nitrobenzene (NB) and aniline (AN) as sole carbon, nitrogen and energy sources, was isolated from an NB and AN contaminated site. Pilot 454 pyrosequencing analysis of the consortium showed that it was mainly made up of Pseudomonas spp. (98%). At 10 °C, the consortium degraded the mixture of 50mg/L NB and 50mg/L AN at a similar rate as those achieved at 20 °C and 30 °C. The biodegradation by-products with different initial NB and AN concentrations at 10 °C were analyzed. Azobenzene, azoxybenzene and acetanilide were observed in NB and AN mixtures degradation. These by-products are generated by the reaction between different intermediates resulting from the NB and AN degradation as well as the parent compounds. To the best of our knowledge, this is the first report confirming the by-products of NB and AN mixture biodegradation by a cold-tolerant microbial consortium.
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Affiliation(s)
- Na Liu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China
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18
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Warnick KH, Wang B, Cliffel DE, Wright DW, Haglund RF, Pantelides ST. Room-temperature reactions for self-cleaning molecular nanosensors. NANO LETTERS 2013; 13:798-802. [PMID: 23320817 DOI: 10.1021/nl304598p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
New sensing techniques for detecting molecules, especially self-cleaning sensors, are in demand. Here we describe a room-temperature process in which a nanostructured substrate catalyzes the reaction of a target molecule with atmospheric oxygen and the reaction energy is absorbed by the substrate, where it can in principle be detected. Specifically, we report first-principles calculations describing a reaction between 2,4-dinitrotoluene (DNT) and atmospheric O(2) catalyzed by Fe-porphyrin at room temperature, incorporating an oxygen into the methyl group of DNT and releasing 1.9 eV per reaction. The atomic oxygen left on the Fe site can be removed by reacting with another DNT molecule, restoring the Fe catalyst.
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Affiliation(s)
- Keith H Warnick
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37235, USA.
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19
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Lorenz A, Rylott EL, Strand SE, Bruce NC. Towards engineering degradation of the explosive pollutant hexahydro-1,3,5-trinitro-1,3,5-triazine in the rhizosphere. FEMS Microbiol Lett 2013; 340:49-54. [DOI: 10.1111/1574-6968.12072] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 12/27/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Astrid Lorenz
- Department of Biology; Centre for Novel Agricultural Products; University of York; York; UK
| | - Elizabeth L. Rylott
- Department of Biology; Centre for Novel Agricultural Products; University of York; York; UK
| | - Stuart E. Strand
- Department of Civil and Environmental Engineering; University of Washington; Seattle; WA; USA
| | - Neil C. Bruce
- Department of Biology; Centre for Novel Agricultural Products; University of York; York; UK
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20
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Procópio A, Procópio R, Pizzirani-Kleiner A, Melo I. Diversity of propanil-degrading bacteria isolated from rice rhizosphere and their potential for plant growth promotion. GENETICS AND MOLECULAR RESEARCH 2012; 11:2021-34. [DOI: 10.4238/2012.august.6.6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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de Las Heras A, Chavarría M, de Lorenzo V. Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol 2011; 82:287-99. [PMID: 21923773 DOI: 10.1111/j.1365-2958.2011.07825.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulation of the DNT pathway for biodegradation of 2,4-dinitrotoluene of Burkholderia sp. DNT has been examined by exporting each of its components to Pseudomonas putida KT2440. The cognate regulator DntR does not respond to the pathway substrate, but to the non-substrate salicylate. In order to examine whether such a response to an unrelated inducer was specific or rather a vestige of a previous evolutionary stage, the complete dnt complement or parts of it were expressed functionally for accumulation of various metabolic intermediates. Their effect on expression of dnt genes was then followed both biochemically and by means of a luminescent reporter engineered in the surrogate host. DntR was not only unresponsive to DNT biodegradation products, but it also failed to influence expression of dnt genes at all. Comparison of the dntR/dntA divergent promoter region with similar ones found in various catabolic systems indicated that the leading segment of the DNT biodegradation pathway evolved from a matching portion of naphthalene biodegradation routes existing in other bacteria. That a useless but still active transcriptional factor occurs along enzymes that have already evolved a new substrate specificity suggests that emergence of novel catalytic abilities precedes their submission to cognate regulatory devices, not vice versa.
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Affiliation(s)
- Aitor de Las Heras
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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22
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Hudcova T, Halecky M, Kozliak E, Stiborova M, Paca J. Aerobic degradation of 2,4-dinitrotoluene by individual bacterial strains and defined mixed population in submerged cultures. JOURNAL OF HAZARDOUS MATERIALS 2011; 192:605-613. [PMID: 21665364 DOI: 10.1016/j.jhazmat.2011.05.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/05/2011] [Accepted: 05/20/2011] [Indexed: 05/30/2023]
Abstract
The degradation efficiencies of isomeric mononitrotoluenes (2- and 4-NTs) and dinitrotoluenes (2,4-DNT and 2,6-DNT) by either individual bacterial strains (Bacillus cereus NDT4, Pseudomonas putida NDT1, Pseudomonas fluorescens NDT2, and Achromobacter sp. NDT3) or their mixture were compared in submerged batch cultivations. The mixed culture degraded 2,4-DNT nearly 50 times faster than any of the individual strains. The mixed culture also demonstrated significantly shorter lag periods in 2,4-DNT degradation, a lack of nitrite or organic intermediates accumulation in the liquid medium and the ability to degrade a broader spectrum of nitrotoluenes over a wider concentration range. The presence of both readily degradable 2-NT (or 4-NT) and poorly degradable 2,6-DNT in the medium negatively affected 2,4-DNT biodegradation. However, the mixed bacterial culture still effectively degraded 2,4-DNT with only slightly lower rates under these unfavorable conditions, thus showing potential for the remediation of 2,4-DNT contaminated sites.
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Affiliation(s)
- Tereza Hudcova
- Institute of Chemical Technology, Prague, Department of Fermentation Chemistry and Bioengineering, Technicka 5, 166 28 Prague, Czech Republic
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Paca J, Halecky M, Hudcova T, Paca J, Stiborova M, Kozliak E. Factors influencing the aerobic biodegradation of 2,4-dinitrotoluene in continuous packed bed reactors. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2011; 46:1328-1337. [PMID: 21929468 DOI: 10.1080/10934529.2011.606422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Factors affecting continuous 2,4-DNT degradation by an immobilized mixed microbial culture were investigated including the cell adaptation to this toxic substrate, 4-NT co-degradation, packing material porosity and substrate mass loading. Experiments were carried out in two packed bed reactors, with poraver (porous glass) and expanded slate as packing materials, using a concurrent water-air flow with ample oxygen. Running the system as a batch reactor with re-circulated medium showed that the immobilized cells adapted to higher 2,4-DNT concentrations yielding higher substrate biodegradation rates. The 2,4-DNT removal rate further increased, up to 180-265 mg L(-1)d(-1), when the immobilized biomass cultivation was switched to a continuous mode. The type of the packing material influenced the 2,4-DNT removal rate, apparently due to the difference in biofilm development. Significant changes in the biofilm composition were observed compared to the original inoculum despite poor biofilm growth.
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Affiliation(s)
- Jan Paca
- Institute of Chemical Technology, Department of Fermentation Chemistry and Bioengineering, Prague, Czech Republic.
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24
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Biodegradation of aromatic compounds: current status and opportunities for biomolecular approaches. Appl Microbiol Biotechnol 2010; 85:207-28. [PMID: 19730850 DOI: 10.1007/s00253-009-2192-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/05/2009] [Accepted: 08/05/2009] [Indexed: 02/03/2023]
Abstract
Biodegradation can achieve complete and cost-effective elimination of aromatic pollutants through harnessing diverse microbial metabolic processes. Aromatics biodegradation plays an important role in environmental cleanup and has been extensively studied since the inception of biodegradation. These studies, however, are diverse and scattered; there is an imperative need to consolidate, summarize, and review the current status of aromatics biodegradation. The first part of this review briefly discusses the catabolic mechanisms and describes the current status of aromatics biodegradation. Emphasis is placed on monocyclic, polycyclic, and chlorinated aromatic hydrocarbons because they are the most prevalent aromatic contaminants in the environment. Among monocyclic aromatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene; phenylacetic acid; and structurally related aromatic compounds are highlighted. In addition, biofilms and their applications in biodegradation of aromatic compounds are briefly discussed. In recent years, various biomolecular approaches have been applied to design and understand microorganisms for enhanced biodegradation. In the second part of this review, biomolecular approaches, their applications in aromatics biodegradation, and associated biosafety issues are discussed. Particular attention is given to the applications of metabolic engineering, protein engineering, and "omics" technologies in aromatics biodegradation.
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25
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Mrozik A, Piotrowska-Seget Z. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol Res 2009; 165:363-75. [PMID: 19735995 DOI: 10.1016/j.micres.2009.08.001] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/29/2009] [Accepted: 08/01/2009] [Indexed: 11/26/2022]
Abstract
The contamination of soil with aromatic compounds is of particular environmental concern as they exhibit carcinogenic and mutagenic properties. One of the methods of their removal from soil is bioaugmentation, defined as a technique for improvement of the degradative capacity of contaminated areas by introduction of specific competent strains or consortia of microorganisms. The efficiency of bioaugmentation is determined by many abiotic and biotic factors discussed in this paper. The first include chemical structure, concentration and availability of pollutants as well as physico-chemical properties of soil. In turn, among biotic factors the most important is the selection of proper microorganisms that can not only degrade contaminants but can also successfully compete with indigenous microflora. Several strategies are being developed to make augmentation a successful technology particularly in soils without degrading indigenous microorganisms. These approaches involve the use of genetically engineered microorganisms and gene bioaugmentation. The enhancement of bioaugmentation may be also achieved by delivering suitable microorganisms immobilized on various carriers or use of activated soil.
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Affiliation(s)
- Agnieszka Mrozik
- Department of Biochemistry, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland.
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26
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Urgun-Demirtas M, Stark B, Pagilla K. Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants. Crit Rev Biotechnol 2008; 26:145-64. [PMID: 16923532 DOI: 10.1080/07388550600842794] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.
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Affiliation(s)
- Meltem Urgun-Demirtas
- Department of Chemical and Environmental Engineering, Illinois Institute of Technology, Chicago, 60616, USA
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27
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Mapelli V, Olsson L, Nielsen J. Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology. Trends Biotechnol 2008; 26:490-7. [DOI: 10.1016/j.tibtech.2008.05.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 05/26/2008] [Accepted: 05/28/2008] [Indexed: 10/21/2022]
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28
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Wu CH, Hwang YC, Lee W, Mulchandani A, Wood TK, Yates MV, Chen W. Detection of recombinant Pseudomonas putida in the wheat rhizosphere by fluorescence in situ hybridization targeting mRNA and rRNA. Appl Microbiol Biotechnol 2008; 79:511-8. [DOI: 10.1007/s00253-008-1438-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 02/21/2008] [Accepted: 02/29/2008] [Indexed: 11/30/2022]
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Chauhan A, Fazlurrahman, Oakeshott JG, Jain RK. Bacterial metabolism of polycyclic aromatic hydrocarbons: strategies for bioremediation. Indian J Microbiol 2008; 48:95-113. [PMID: 23100704 DOI: 10.1007/s12088-008-0010-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/21/2008] [Accepted: 02/04/2008] [Indexed: 10/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are compounds of intense public concern due to their persistence in the environment and potentially deleterious effects on human, environmental and ecological health. The clean up of such contaminants using invasive technologies has proven to be expensive and more importantly often damaging to the natural resource properties of the soil, sediment or aquifer. Bioremediation, which exploits the metabolic potential of microbes for the clean-up of recalcitrant xenobiotic compounds, has come up as a promising alternative. Several approaches such as improvement in PAH solubilization and entry into the cell, pathway and enzyme engineering and control of enzyme expression etc. are in development but far from complete. Successful application of the microorganisms for the bioremediation of PAH-contaminated sites therefore requires a deeper understanding of the physiology, biochemistry and molecular genetics of potential catabolic pathways. In this review, we briefly summarize important strategies adopted for PAH bioremediation and discuss the potential for their improvement.
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Affiliation(s)
- Archana Chauhan
- Institute of Microbial Technology, Sector-39A, Chandigarh, India
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Villas-Bôas SG, Bruheim P. The Potential of Metabolomics Tools in Bioremediation Studies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:305-13. [PMID: 17883341 DOI: 10.1089/omi.2007.0005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
As a post-genomics tool, metabolomics is a young and vibrant field of science in its exponential growth phase. Metabolome analysis has become very popular recently, and novel techniques for acquiring and analyzing metabolomics data continue to emerge that are useful for a variety of biological studies. The bioremediation field has a lot to gain from the advances in this emerging area. Thus, this review article focuses on the potential of various experimental and conceptual approaches developed for metabolomics to be applied in bioremediation research, such as strategies for elucidation of biodegradation pathways using isotope distribution analysis and molecular connectivity analysis, the assessment of mineralization process using metabolic footprinting analysis, and the improvement of the biodegradation process via metabolic engineering. We demonstrate how the use of metabolomics tools can significantly extend and enhance the power of existing bioremediation approaches by providing a better overview of the biodegradation process.
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Liu L, Jiang CY, Liu XY, Wu JF, Han JG, Liu SJ. Plant-microbe association for rhizoremediation of chloronitroaromatic pollutants with Comamonas sp. strain CNB-1. Environ Microbiol 2007; 9:465-73. [PMID: 17222144 DOI: 10.1111/j.1462-2920.2006.01163.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Comamonas sp. strain CNB-1, isolated from activated sludge and having a strong ability to degrade 4-chloronitrobenzene (4CNB), was applied for rhizoremediation of 4CNB-polluted soil through association with alfalfa. Confocal laser scanning microscopy revealed that strain CNB-1 successfully colonized alfalfa roots. Determination of strain CNB-1 populations by cultivation method and by quantitative competitive PCR technique targeting the chloronitrobenzene nitroreductase gene showed that the population of strain CNB-1 in the rhizosphere was about 10-100 times higher than that in the bulk soil. Gnotobiotic and outdoor experiments showed that pollutant 4CNB was completely removed within 1 or 2 days after 4CNB application into soil, and that its phytotoxicity to alfalfa was eliminated by inoculation of strain CNB-1. Results from PCR-denaturing gradient gel electrophoresis and analysis of 16S rRNA gene libraries revealed that the indigenous soil microbial community mainly consisted of alphaproteobacteria, betaproteobacteria, gammaproteobacteria, the CFB bacteria (Cytophaga-Flavabacterium-Bacteriodes), and Acidobacteria. This microbial community was not significantly influenced by inoculation of strain CNB-1. Thus, this study has developed a Comamonas-alfalfa system for rhizoremediation of 4CNB.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
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