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Tembeni B, Idowu OE, Benrkia R, Boutahiri S, Olatunji OJ. Biotransformation of selected secondary metabolites by Alternaria species and the pharmaceutical, food and agricultural application of biotransformation products. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:46. [PMID: 39158793 PMCID: PMC11333692 DOI: 10.1007/s13659-024-00469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/04/2024] [Indexed: 08/20/2024]
Abstract
Biotransformation is a process in which molecules are modified in the presence of a biocatalyst or enzymes, as well as the metabolic alterations that occur in organisms from exposure to the molecules. Microbial biotransformation is an important process in natural product drug discovery as novel compounds are biosynthesised. Additionally, biotransformation products offer compounds with improved efficacy, solubility, reduced cytotoxic and allows for the understanding of structure activity relationships. One of the driving forces for these impeccable findings are associated with the presence of cytochrome P450 monooxygenases that is present in all organisms such as mammals, bacteria, and fungi. Numerous fungal strains have been used and reported for their ability to biotransform different compounds. This review focused on studies using Alternaria species as biocatalysts in the biotransformation of natural product compounds. Alternaria species facilitates reactions that favour stereoselectivity, regioselectivity under mild conditions. Additionally, microbial biotransformation products, their application in food, pharmaceutical and agricultural sector is discussed in this review.
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Affiliation(s)
- Babalwa Tembeni
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco.
| | | | - Rachid Benrkia
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Salima Boutahiri
- African Genome Center, Mohammed VI Polytechnic University, Benguerir, Morocco
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2
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Hu S, Xu C, Xie Y, Ma L, Niu Q, Han G, Huang J. Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168723. [PMID: 38008322 DOI: 10.1016/j.scitotenv.2023.168723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/15/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.
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Affiliation(s)
- Shunli Hu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Chuangchuang Xu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Lu Ma
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Guomin Han
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China.
| | - Junwei Huang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China.
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3
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Iasakov T. Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D). Int J Mol Sci 2023; 24:14370. [PMID: 37762674 PMCID: PMC10531765 DOI: 10.3390/ijms241814370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.
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Affiliation(s)
- Timur Iasakov
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia
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Wang Y, Tian YS, Gao JJ, Xu J, Li ZJ, Fu XY, Han HJ, Wang LJ, Zhang WH, Deng YD, Qian C, Zuo ZH, Wang B, Peng RH, Yao QH. Complete biodegradation of the oldest organic herbicide 2,4-Dichlorophenoxyacetic acid by engineering Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131099. [PMID: 36868133 DOI: 10.1016/j.jhazmat.2023.131099] [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: 11/12/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
After nearly 80 years of extensive application, the oldest organic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has caused many problems of environmental pollution and ecological deterioration. Bioremediation is an ideal method for pollutant treatment. However, difficult screening and preparation of efficient degradation bacteria have largely hindered its application in 2,4-D remediation. We have created a novel engineering Escherichia coli with a reconstructed complete degradation pathway of 2,4-D to solve the problem of screening highly efficient degradation bacteria in this study. The results of fluorescence quantitative PCR demonstrated that all nine genes in the degradation pathway were successfully expressed in the engineered strain. The engineered strains can quickly and completely degrade 0.5 mM 2, 4-D within 6 h. Inspiring, the engineered strains grew with 2,4-D as the sole carbon source. By using the isotope tracing method, the metabolites of 2,4-D were found incorporated into the tricarboxylic acid cycle in the engineering strain. Scanning electron microscopy showed that 2,4-D had less damage on the engineered bacteria than the wild-type strain. Engineered strain can also rapidly and completely remedy 2,4-D pollution in natural water and soil. Assembling the metabolic pathways of pollutants through synthetic biology was an effective method to create pollutant-degrading bacteria for bioremediation.
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Affiliation(s)
- Yu Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong-Sheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jian-Jie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhen-Jun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiao-Yan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong-Juan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li-Juan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wen-Hui Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yong-Dong Deng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Cen Qian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhi-Hao Zuo
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
| | - Ri-He Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
| | - Quan-Hong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
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Zhang X, Geng K, Wu N, Hu G, Fan B, He J, Qiao W. Sustained anaerobic degradation of 4-chloro-2-methylphenoxyacetic acid by acclimated sludge in a continuous-flow reactor. CHEMOSPHERE 2023; 330:138749. [PMID: 37086982 DOI: 10.1016/j.chemosphere.2023.138749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
4-Chloro-2-methylphenoxyacetic acid (MCPA) is a widely used herbicide across the world. MCPA is persistent and easily transports into anoxic environment, such as groundwater, sediments and deep soils. However, little research on anaerobic microbial degradation of MCPA was carried out. The functional microorganisms as well as the catabolic pathway are still unknown. In this research, an anaerobic MCPA-degrading bacterial consortium was enriched from the river sediment near a pesticide-manufacturing plant. After about 6 months' acclimation, the MCPA transformation rate of the consortium reached 4.32 μmol g-1 day-1, 25 times faster than that of the original sludge. 96% of added MCPA (2.5 mM) was degraded within 9 d of incubation. Three metabolites including 4-chloro-2-methylphenol (MCP), 2-methylphenol (2-MP) and phenol were identified during the anaerobic degradation of MCPA. An anaerobic catabolic pathway was firstly proposed: firstly, MCPA was transformed to MCP via the cleavage of the aryl ether, then MCP was reductively dechlorinated to 2-MP which was further demethylated to phenol. The 16S rRNA gene amplicon sequencing revealed a substantial shift in the bacterial community composition after the acclimation. SBR1031, Acidaminococcaceae, Aminicenantales, Syntrophorhabdus, Acidaminobacter, Bacteroidetes_vadinHA17, Methanosaeta, Bathyarchaeia, KD4-96, Anaeromyxobacter, and Dehalobacter were significantly increased in the enriched consortium after acclimation, and positively correlated with the anaerobic degradation of MCPA as suggested by heat map correlation analysis. This study provides a basis for further elucidation of the anaerobic catabolism of MCPA, and contributes to developing efficient and low-cost anaerobic treatment technologies for MCPA pollution.
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Affiliation(s)
- Xuan Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Keke Geng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Ningning Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Gang Hu
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Ben Fan
- College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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Vanitha TK, Suresh G, Bhandi MM, Mudiam MKR, Mohan SV. Microbial degradation of organochlorine pesticide: 2,4-Dichlorophenoxyacetic acid by axenic and mixed consortium. BIORESOURCE TECHNOLOGY 2023; 382:129031. [PMID: 37037331 DOI: 10.1016/j.biortech.2023.129031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/31/2023]
Abstract
The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.
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Affiliation(s)
- T K Vanitha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - G Suresh
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India
| | - Murali Mohan Bhandi
- Analytical & Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohana Krishna Reddy Mudiam
- Analytical & Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Magnoli K, Carranza CS, Aluffi ME, Benito N, Magnoli CE, Barberis CL. Survey of organochlorine-tolerant culturable mycota from contaminated soils, and 2,4-D removal ability of Penicillium species in synthetic wastewater. Fungal Biol 2023; 127:891-899. [PMID: 36746561 DOI: 10.1016/j.funbio.2022.11.003] [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: 07/18/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
Agrochemical wastewater, which is produced by the extensive use of herbicides, has become a serious environmental pollutant. In this study, culturable mycota were isolated from soils contaminated with herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-chloro-2-methylphenoxyacetic acid (MCPA), and their ability to tolerate and remove 2,4-D was assessed. The mycota were isolated on solid medium supplemented with 10 mmol L-1 of MCPA or 2,4-D. Tolerance and removal assays were performed in synthetic wastewater, and removal was quantified by HPLC-UV and MS/MS. Fusarium spp., Aspergillus spp., and Penicillium spp. were the most frequently isolated genera. Six Penicillium strains were able to tolerate up to 25 mmol L-1 of 2,4-D. Within this group, two P. crustosum strains (RCP4 and RCP13) degraded more than 50% of the 2,4-D in the medium during the first 7 days of incubation. Removal percentages reached 54% for RCP4 and 75% for RCP13 after 14 days. These two strains, therefore, could potentially be considered for the design of bioaugmentation strategies aimed at reducing contamination by 2,4-D in wastewater.
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Affiliation(s)
- Karen Magnoli
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina; Fellowship of CONICET, Argentina
| | - Cecilia Soledad Carranza
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Melisa Eglé Aluffi
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina; Fellowship of CONICET, Argentina
| | - Nicolás Benito
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina; Fellowship of CONICET, Argentina
| | - Carina Elizabeth Magnoli
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina; Member of the Research Career of CONICET, Argentina
| | - Carla Lorena Barberis
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET), Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional Nº 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina; Member of the Research Career of CONICET, Argentina.
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8
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Pan D, Xu Y, Ni Y, Zhang H, Hua R, Wu X. The efficient persistence and migration of Cupriavidus gilardii T1 contribute to the removal of MCPA in laboratory and field soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119220. [PMID: 35358633 DOI: 10.1016/j.envpol.2022.119220] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
The application of exogenous biodegradation strains in pesticide-polluted soils encounters the challenges of migration and persistence of inoculants. In this study, the degradation characteristics, vertical migration capacity, and microbial ecological risk assessment of an enhanced green fluorescent protein (EGFP)-tagged 2-Methyl-4-chlorophenoxyacetic acid (MCPA)-degrading strain Cupriavidus gilardii T1 (EGFP) were investigated in the laboratory and field soils. The optimum remediation conditions for T1 (EGFP) was characterized in soils. Meanwhile, leaching experiments showed that T1 (EGFP) migrated vertically downwards in soil and contribute to the degradation of MCPA at different depths. After inoculation with T1 (EGFP), a high expression levels of EGFP gene was observed at 28 d in the laboratory soil and at 45 d in the field soil. The degradation rates of MCPA were ≥ 60% in the laboratory soil and ≥ 48% in the field soil, indicating that T1 (EGFP) can efficiently and continuously remove MCPA in both laboratory and field conditions. In addition, the inoculation of T1 (EGFP) not only showed no significant impact on the soil microbial community structure but also can alleviate the negative effects induced by MCPA to some extent. Overall, our findings suggested that T1 (EGFP) strain is an ecologically safe resource for the in situ bioremediation of MCPA-contaminated soils.
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Affiliation(s)
- Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Yue Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Yaxin Ni
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China.
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A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis. Appl Environ Microbiol 2021; 87:e0156221. [PMID: 34524896 DOI: 10.1128/aem.01562-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[13C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.
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Complete Genome Sequence of Achromobacter Strain ES-001, a Betaproteobacterium Associated with a Cellulolytic Soil Community. Microbiol Resour Announc 2021; 10:e0082821. [PMID: 34617787 PMCID: PMC8496361 DOI: 10.1128/mra.00828-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of the soilborne bacterium Achromobacter strain ES-001, assembled from Illumina NextSeq and Nanopore MinION reads, is rich in genes predicted to encode iron, arsenic, and hydrocarbon metabolism, as well as type 6 secretion components. The sequenced genome will aid in determining the roles of noncellulolytic species in cellulose-enriched environments.
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Mishra B, Varjani S, Kumar G, Awasthi MK, Awasthi SK, Sindhu R, Binod P, Rene ER, Zhang Z. Microbial approaches for remediation of pollutants: Innovations, future outlook, and challenges. ENERGY & ENVIRONMENT 2021; 32:1029-1058. [DOI: 10.1177/0958305x19896781] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Environmental contamination with persistent organic pollutants has emerged as a serious threat of pollution. Bioremediation is a key to eliminate these harmful pollutants from the environment and has gained the interest of researchers during the past few decades. Scientific knowledge upon microbial interactions with individual pollutants over the past decades has helped to abate environmental pollution. Traditional bioremediation approaches have limitations for their applications; hence, it is essential to discover new bioremediation approaches with biotechnological interventions for best results. The developments in various methodologies are expected to increase the efficiency of bioremediation techniques and provide environmentally sound strategies. This paper deals with the profiling of microorganisms present in polluted sites using various techniques such as culture-based approaches and omics-based approaches. Besides this, it also provides up-to-date scientific literature on the microbial electrochemical technologies which are nowadays considered as the best approach for remediation of pollutants. Detailed information about future outlook and challenges to evaluate the effect of various treatment technologies for remediation of pollutants has been discussed.
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Affiliation(s)
- Bishwambhar Mishra
- Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Hyderabad, India
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, India
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
| | - Raveendran Sindhu
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Parameswaran Binod
- CSIR–National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, India
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology, IHE Delft Institute of Water Education, Delft, The Netherlands
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A& F University, Shaanxi Province, PR China
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12
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Carles L, Martin-Laurent F, Devers M, Spor A, Rouard N, Beguet J, Besse-Hoggan P, Batisson I. Potential of preventive bioremediation to reduce environmental contamination by pesticides in an agricultural context: A case study with the herbicide 2,4-D. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125740. [PMID: 33848793 DOI: 10.1016/j.jhazmat.2021.125740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
One of the major problems with pesticides is linked to the non-negligible proportion of the sprayed active ingredient that does not reach its intended target and contaminates environmental compartments. Here, we have implemented and provided new insights to the preventive bioremediation process based on the simultaneous application of the pesticide with pesticide-degrading microorganisms to reduce the risk of leaching into the environment. This study pioneers such a practice, in an actual farming context. The 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) and one of its bacterial mineralizing-strains (Cupriavidus necator JMP134) were used as models. The 2,4-D biodegradation was studied in soil microcosms planted with sensitive (mustard) and insensitive (wheat) plants. Simultaneous application of a 2,4-D commercial formulation (DAM®) at agricultural recommended doses with 105 cells.g-1 dw of soil of the JMP134 strain considerably accelerated mineralization of the herbicide since its persistence was reduced threefold for soil supplemented with the mineralizing bacterium without reducing the herbicide efficiency. Furthermore, the inoculation of the Cupriavidus necator strain did not significantly affect the α- and β-diversity of the bacterial community. By tackling the contamination immediately at source, the preventive bioremediation process proves to be an effective and promising way to reduce environmental contamination by agricultural pesticides.
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Affiliation(s)
- Louis Carles
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France.
| | - Fabrice Martin-Laurent
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marion Devers
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aymé Spor
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jérémie Beguet
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pascale Besse-Hoggan
- Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Isabelle Batisson
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France
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13
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Marussi G, Vione D. Secondary Formation of Aromatic Nitroderivatives of Environmental Concern: Photonitration Processes Triggered by the Photolysis of Nitrate and Nitrite Ions in Aqueous Solution. Molecules 2021; 26:2550. [PMID: 33925664 PMCID: PMC8124604 DOI: 10.3390/molecules26092550] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Aromatic nitroderivatives are compounds of considerable environmental concern, because some of them are phytotoxic (especially the nitrophenols, and particularly 2,4-dinitrophenol), others are mutagenic and potentially carcinogenic (e.g., the nitroderivatives of polycyclic aromatic hydrocarbons, such as 1-nitropyrene), and all of them absorb sunlight as components of the brown carbon. The latter has the potential to affect the climatic feedback of atmospheric aerosols. Most nitroderivatives are secondarily formed in the environment and, among their possible formation processes, photonitration upon irradiation of nitrate or nitrite is an important pathway that has periodically gained considerable attention. However, photonitration triggered by nitrate and nitrite is a very complex process, because the two ionic species under irradiation produce a wide range of nitrating agents (such as •NO2, HNO2, HOONO, and H2OONO+), which are affected by pH and the presence of organic compounds and, in turn, deeply affect the nitration of aromatic precursors. Moreover, aromatic substrates can highly differ in their reactivity towards the various photogenerated species, thereby providing different behaviours towards photonitration. Despite the high complexity, it is possible to rationalise the different photonitration pathways in a coherent framework. In this context, this review paper has the goal of providing the reader with a guide on what to expect from the photonitration process under different conditions, how to study it, and how to determine which pathway(s) are prevailing in the formation of the observed nitroderivatives.
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Affiliation(s)
- Giovanna Marussi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy;
| | - Davide Vione
- Dipartimento di Chimica, Università degli Studi di Torino, Via Pietro Giuria 5, 10125 Torino, Italy
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Balakrishnan A, Gopalram K, Appunni S. Photocatalytic degradation of 2,4-dicholorophenoxyacetic acid by TiO 2 modified catalyst: kinetics and operating cost analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10.1007/s11356-021-12928-4. [PMID: 33641092 DOI: 10.1007/s11356-021-12928-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Effective pesticide remediation technology demands amendments in the advanced oxidation process for its continuous treatment and catalyst recovery. The evidence of 2,4-dichlorophenoxyacetic acid (2,4-D), an herbicide in water bodies, poses a major environmental threat to both humans and aquatic organisms. In the present study, a recirculation type photocatalytic reactor was developed to treat 2,4-dichlorophenoxyacetic acid using chitosan-TiO2 beads prepared via impregnation method under UV light. At optimized conditions, chitosan-TiO2 beads showed a maximum photocatalytic degradation of 86% than commercial TiO2 (65%) and followed pseudo first-order reaction. The 2,4-D degradation follows pseudo first-order kinetics under UV irradiation with a rate constant of 0.12 h-1, and the intermediates were identified using LCMS analysis. The total operational cost of the chitosan-TiO2 catalyst was found to be profitable (Rs. 1323 for 2 L) than that of TiO2 (Rs. 1679) at optimized conditions. The beads were reusable up to 4 consecutive cycles without loss in efficiency. This study briefs photocatalytic removal of 2,4-dichlorophenoxyacetic acid in a recirculation-type reactor for its reliability, low cost, efficiency, reusability, and commercialization.
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Affiliation(s)
- Akash Balakrishnan
- Department of Chemical Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, 603 203, Kanchipuram, Chennai, Tamil Nadu, India
| | - Keerthiga Gopalram
- Department of Chemical Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, 603 203, Kanchipuram, Chennai, Tamil Nadu, India.
| | - Sowmya Appunni
- Department of Chemical Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, 603 203, Kanchipuram, Chennai, Tamil Nadu, India
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Magnoli K, Carranza CS, Aluffi ME, Magnoli CE, Barberis CL. Herbicides based on 2,4-D: its behavior in agricultural environments and microbial biodegradation aspects. A review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:38501-38512. [PMID: 32770339 DOI: 10.1007/s11356-020-10370-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
One of the main herbicides used in the agricultural environments is 2,4-dichlorophenoxyacetic acid (2,4-D). It is a synthetic plant hormone auxin employed in many crops including rice, wheat, sorghum, sugar cane, and corn to control wide leaf weeds. The indiscriminate use of pesticides can produce numerous damages to the environment. Therefore, this review has the objective to provide an overview on the main characteristics of the herbicides based on 2,4-D, mostly on the role of microorganisms in its degradation and its main degradation metabolite, 2,4- dichlorophenol (2,4-DCP). The remediation processes carried out by microorganisms are advantageous to avoid the pollution of the environment as well as to safeguard the population health.
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Affiliation(s)
- Karen Magnoli
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET). Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional N° 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Cecilia Soledad Carranza
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET). Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional N° 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Melisa Eglé Aluffi
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET). Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional N° 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Carina Elizabeth Magnoli
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET). Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional N° 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina
| | - Carla Lorena Barberis
- Instituto de Investigación en Micología y Micotoxicología (IMICO-CONICET). Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico, Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta Nacional N° 36 Km 601, 5800, Río Cuarto, Córdoba, Argentina.
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16
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Rosado-Flores MF, González-Prieto JM, Mireles-Martínez M, Torres-Ortega JA, Rosas-García NM, Villegas-Mendoza JM. Identificación de microorganismos aislados de suelos agrícolas con capacidad de tolerar 2.4-D y malatión. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
En el presente estudio, se analizó la diversidad microbiana de los suelos agrícolas de las localidades de Río Bravo y la Estación Cuauhtémoc en el estado de Tamaulipas y en los límites de Dolores Hidalgo en el estado de Guanajuato. Los plaguicidas utilizados fueron 2,4-D y malatión, con los que se establecieron pruebas preselectivas para el aislamiento de los microorganismos y su tolerancia. Para la identificación de las bacterias se amplificó el gen 16S y para los hongos la región ITS. El género bacteriano Pseudomonas, así como el género fúngico Penicillium fueron los de mayor abundancia en las muestras analizadas. Los resultados indicaron que las cepas tolerantes fueron Pseudomonas aeruginosa, Stenotrophomonas pavanii y Acinetobacter lactucae creciendo a una concentración > 2.0 g L-1 de 2,4-D y > 1.0 g L-1 de malatión. Así como Fusarium sp., a 2.0 g L-1 de malatión y 0.9 g L-1 de 2,4-D y el hongo Talaromyces variabilis con un crecimiento a 3.1 g L-1 de malatión. Para el caso de S. pavanii, A. Lactucae y T. variabilis no existen reportes de tolerancia a los plaguicidas mencionados, sin embargo, en este trabajo se demuestra por primera vez que pueden ser utilizados en técnicas de biorremediación de suelos.
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Zhang L, Hang P, Zhou XY, Qiao WJ, Jiang JD. Enantioselective Catabolism of the Two Enantiomers of the Phenoxyalkanoic Acid Herbicide Dichlorprop by Sphingopyxis sp. DBS4. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6967-6976. [PMID: 32530641 DOI: 10.1021/acs.jafc.0c01066] [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
Dichlorprop [(RS)-2-(2,4-dichlorophenoxy)propanoic acid; DCPP], an important phenoxyalkanoic acid herbicide (PAAH), is extensively used in the form of racemic mixtures (Rac-DCPP), and the environmental fates of both DCPP enantiomers [(R)-DCPP and (S)-DCPP] mediated by microorganisms are of great concern. In this study, a bacterial strain Sphingopyxis sp. DBS4 was isolated from contaminated soil and was capable of utilizing both (R)-DCPP and (S)-DCPP as the sole carbon source for growth. Strain DBS4 preferentially catabolized (S)-DCPP as compared to (R)-DCPP. The optimal conditions for Rac-DCPP degradation by strain DBS4 were 30 °C and pH 7.0. In addition to Rac-DCPP, other PAAHs such as (RS)-2-(4-chloro-2-methylphenoxy)propanoic acid, 2,4-dichlorophenoxyacetic acid, 4-chloro-2-methylphenoxyacetic acid, and 2,4-dichlorophenoxyacetic acid butyl ester could also be catabolized by strain DBS4. Bioremediation of Rac-DCPP-contaminated soil by inoculation of strain DBS4 exhibited an effective removal of both (R)-DCPP and (S)-DCPP from the soil. Due to its broad substrate spectrum, strain DBS4 showed great potential in the bioremediation of PAAH-contaminated sites.
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Ping Hang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xi-Yi Zhou
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Wen-Jing Qiao
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, 210095 Nanjing, China
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Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species. Sci Rep 2019; 9:15271. [PMID: 31649302 PMCID: PMC6813343 DOI: 10.1038/s41598-019-51707-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/07/2019] [Indexed: 11/08/2022] Open
Abstract
Allium species are popular vegetables in China and possess antifungal and antibacterial activities. This study aimed to compare the endophytic bacterial community in the four crucial Allium species in China, Chinese leek (CL), garlic (GA), onion (ON,) and Welsh onion (WO), using sequences of the V3–V4 region of the bacterial 16S rRNA gene. A total of 1,036,637 high-quality sequences and 719 operational taxonomic units (OTUs) were obtained across all libraries. A total of 20 phyla, 50 classes, 80 orders, 134 families, and 234 genera were identified. Among them, 18 OTUs and 19 genera were shared among the four Allium species. Proteobacteria (42.68%) and Bacteroidetes (20.18%) were the dominant phyla in CL, while one unclassified (>70%) was the dominant phyla in the other three Allium species. The alpha-diversity analysis showed the bacterial richness and diversity in CL were significantly higher than those in the other three Allium species. Principal coordinate analysis (PCA) showed endophytic bacterial communities in GA, WO, and ON were more similar than those in CL. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed endophytic bacteria mostly enriched in Membrane Transport, Amino Acid Metabolism and Carbohydrate Metabolism pathway. 17 of the 23 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories and 159 of the 206 lower-level KEGG pathways in CL were significantly higher than those in the other three Allium species. Pearson’s correlation indicated that KEGG pathways with significant differences among the Allium species were closely related to the bacterial genera with significant differences between the Allium species. The findings of our study provided insight into the complex endophytic microbial communities in Allium species.
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Aguiar LM, Dos Santos JB, Barroso GM, Laia MLD, Gonçalves JF, da Costa VAM, Brito LA. Influence of 2,4-D residues on the soil microbial community and growth of tree species. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 22:69-77. [PMID: 31342787 DOI: 10.1080/15226514.2019.1644289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2,4-D (2,4-dichlorophenoxyacetic acid) has low half-life in the soil, but it is capable of altering the soil microbial community. The objective of this study was to evaluate the influence of 2,4-D residues on the structure of the soil microbial community and the growth of tree species. The tolerance and phytoremediation potential of tree species were evaluated. The microbial analysis was performed by T-RFLP. The 2,4-D herbicide reduced the plant height of K. lathrophyton, number of leaves of C. ferrea and K. lathrophyton and root dry matter allocation for C. brasiliense, I. striata, P. heptaphyllum, and T. guianensis. Cucumis sativus intoxication on soil contaminated with 2,4-D was not significant. The structure of Fungi community in the rhizospheric soils of C. ferrea was altered. The herbicide 2,4-D increased the diversity of Fungi in rhizospheric soils of P. heptahyllum and R. grandis. Most tree species were tolerant, and the evaluation time was sufficient to remedy 2,4-D. The structures of the microbial communities Archaea, Bacteria, and Fungi were little influenced by 2,4-D. The diversity of the Archaea domain was not affected, the diversity of the Bacteria in Inga striata decreased while the fungi increased in Protium heptaphyllum and Richeria grandis with 2,4-D.
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Affiliation(s)
- Luciana Monteiro Aguiar
- Departamento de Agronomia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - José Barbosa Dos Santos
- Departamento de Agronomia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Gabriela Madureira Barroso
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Marcelo Luiz de Laia
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
| | - Janaína Ferreira Gonçalves
- Departamento de Ciências Agrárias, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brasil
| | | | - Lílian Almeida Brito
- Departamento de Engenharia Florestal, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Brasil
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Removal and Ecotoxicity of 2,4-D and MCPA in Microbial Cultures Enriched with Structurally-Similar Plant Secondary Metabolites. WATER 2019. [DOI: 10.3390/w11071451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The removal of contaminants from the environment can be enhanced by interactions between structurally-related plant secondary metabolites (PSMs), selected xenobiotics and microorganisms. The aim of this study was to investigate the effect of selected PSMs (ferulic acid—FA; syringic acid—SA) on the removal of structurally-similar phenoxy herbicides (PHs): 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA). The study also examines the biodegradation potential of soil bacteria, based on the occurrence of functional tdfA-like genes, and the ecotoxicity of the samples against two test species: Sinapis alba L. and Lepidium sativum L. The microbial cultures spiked with the PSMs demonstrated higher phenoxy acid removal: 97–100% in the case of 2,4-D and 99%–100% for MCPA. These values ranged from 5% to 100% for control samples not amended with FA or SA. The higher herbicide removal associated with PSM spiking can be attributed to acceleration of the microbial degradation processes. Our findings showed that the addition of SA particularly stimulated the occurrence of the total number of tfdA genes, with this presence being higher than that observed in the unamended samples. PSM spiking was also found to have a beneficial effect on ecotoxicity mitigation, reflected in high (102%) stimulation of root growth by the test species.
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Study of 2,4-D Spectral Characteristics and Its Detection in Zizania Latifolia Using Terahertz Time-Domain Spectroscopy. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9112248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D) is a common plant growth regulator, which can remain in food and, with long-term consumption, threaten human health. Therefore, it is necessary to propose an effective detection method. Terahertz time-domain spectroscopy technique (THz-TDS) has good advantages in the quantitative and qualitative analysis of most biomolecules due to its rich fingerprint characteristics. In this paper, density functional theory (DFT) was applied to geometry optimization and frequency vibration calculation of 2,4-D, and THz-TDS was used to quantitatively detect 2,4-D in Zizania latifolia. The results showed that there were three characteristic absorption peaks of 2,4-D at 1.36, 1.60, and 2.38 THz, respectively, and the theoretical spectra were in good consistency with experimental spectra, with slight discrepancies. Additionally, the absorption peak at 1.36 THz had the best absorption characteristics and was chosen as the main peak for 2,4-D quantitative analysis. It was demonstrated that the limits of detection (LOD) of 2,4-D in Zizania latifolia were found to be as low as 5%, the absorbance intensity at 1.36 THz showed a good linear relationship (R2 = 0.9854) with 2,4-D concentration from 5% to 30%, and the recovery was 93.29%–98.75%. Overall, this work enriched the fingerprint database of pesticide molecules on the basis of terahertz spectroscopy and could provide a technical support for the detection of 2,4-D in food by terahertz spectroscopy.
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Serbent MP, Rebelo AM, Pinheiro A, Giongo A, Tavares LBB. Biological agents for 2,4-dichlorophenoxyacetic acid herbicide degradation. Appl Microbiol Biotechnol 2019; 103:5065-5078. [DOI: 10.1007/s00253-019-09838-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/12/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022]
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Urbaniak M, Mierzejewska E, Tankiewicz M. The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA. PeerJ 2019; 7:e6745. [PMID: 30993052 PMCID: PMC6462179 DOI: 10.7717/peerj.6745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/27/2019] [Indexed: 01/04/2023] Open
Abstract
The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.
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Affiliation(s)
- Magdalena Urbaniak
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic.,Faculty of Biology and Environmental Protection, Department of Applied Ecology, University of Lodz, Lodz, lodzkie, Polska
| | - Elżbieta Mierzejewska
- Faculty of Biology and Environmental Protection, Department of Applied Ecology, University of Lodz, Lodz, lodzkie, Polska
| | - Maciej Tankiewicz
- Department of Environmental Toxicology, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
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Zhang H, Yu T, Li J, Wang YR, Wang GL, Li F, Liu Y, Xiong MH, Ma YQ. Two dcm Gene Clusters Essential for the Degradation of Diclofop-methyl in a Microbial Consortium of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12217-12226. [PMID: 30375865 DOI: 10.1021/acs.jafc.8b05382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The metabolism of widely used aryloxyphenoxypropionate herbicides has been extensively studied in microbes. However, the information on the degradation of diclofop-methyl (DCM) is limited, with no genetic and biochemical investigation reported. The consortium L1 of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9 was able to degrade DCM through a synergistic metabolism. To elaborate the molecular mechanism of DCM degradation, the metabolic pathway for DCM was first investigated. DCM was initially transformed by strain JT-3 to diclofop acid and then by strain JT-9 to 2-(4-hydroxyphenoxy) propionic acid as well as 2,4-dichlorophenol. Subsequently, the two dcm gene clusters, dcmAE and dcmB1B2CD, involved in further degradation of 2,4-dichlorophenol, were successfully cloned from strain JT-3, and the functions of each gene product were identified. DcmA, a glutathione-dependent dehalogenase, was responsible for catalyzing the reductive dehalogenation of 2,4-dichlorophenol to 4-chlorophenol, which was then converted by the two-component monooxygenase DcmB1B2 to 4-chlorocatechol as the ring cleavage substrate of the dioxygenase DcmC. In this study, the overall DCM degradation pathway of the consortium L1 was proposed and, particularly, the lower part on the DCP degradation was characterized at the genetic and biochemical levels.
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Affiliation(s)
- Hui Zhang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ting Yu
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Jie Li
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Yi-Ran Wang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Guang-Li Wang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Feng Li
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Yuan Liu
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ming-Hua Xiong
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ying-Qun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute , Nanyang Technological University , 1 Cleantech Loop , Singapore 637141 , Singapore
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Ha DD. Anaerobic degradation of 2,4-dichlorophenoxyacetic acid by Thauera sp. DKT. Biodegradation 2018; 29:499-510. [PMID: 30105582 DOI: 10.1007/s10532-018-9848-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Thauera sp. strain DKT isolated from sediment utilized 2,4-dichlorophenoxyacetic acid (2,4D) and its relative compounds as sole carbon and energy sources under anaerobic conditions and used nitrate as an electron acceptor. The determination of 2,4D utilization at different concentrations showed that the utilization curve fitted well with the Edward model with the maximum degradation rate as 0.017 ± 0.002 mM/day. The supplementation of cosubstrates (glucose, acetate, sucrose, humate and succinate) increased the degradation rates of all tested chemical substrates in both liquid and sediment slurry media. Thauera sp. strain DKT transformed 2,4D to 2,4-dichlorophenol (2,4DCP) through reductive side-chain removal then dechlorinated 2,4DCP to 2-chlorophenol (2CP), 4-chlorophenol (4CP) and phenol before complete degradation. The relative degradation rates by the isolate in liquid media were: phenol > 2,4DCP > 2CP > 4CP > 2,4D ≈ 3CP. DKT augmentation in sediment slurry enhanced the degradation rates of 2,4D and chlorophenols. The anaerobic degradation rates in the slurry were significantly slower compared to the rates in liquid media.
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Affiliation(s)
- Duc Danh Ha
- Dong Thap University, Cao Lanh City, Dong Thap Province, Vietnam.
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Ahmad F, Anwar S, Firdous S, Da-Chuan Y, Iqbal S. Biodegradation of bispyribac sodium by a novel bacterial consortium BDAM: Optimization of degradation conditions using response surface methodology. JOURNAL OF HAZARDOUS MATERIALS 2018; 349:272-281. [PMID: 29438823 DOI: 10.1016/j.jhazmat.2017.12.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/28/2017] [Accepted: 12/27/2017] [Indexed: 06/08/2023]
Abstract
Bispyribac sodium (BS), is a selective, systemic and post emergent herbicide used to eradicate grasses and broad leaf weeds. Extensive use of this herbicide has engendered serious environmental concerns. Hence it is important to develop strategies for bioremediation of BS in a cost effective and environment friendly way. In this study a bacterial consortium named BDAM, comprising three novel isolates Achromobacter xylosoxidans (BD1), Achromobacter pulmonis (BA2), and Ochrobactrum intermedium (BM2), was developed by virtue of its potential for degradation of BS. Different culture conditions (temperature, pH and inoculum size) were optimized for degradation of BS by the consortium BDAM and the mutual interactions of these parameters were analysed using a 23 full factorial central composite design (CCD) based on Response Surface Methodology (RSM). The optimal values for temperature, pH and inoculum size were found to be 40 °C, 8 and 0.4 g/L respectively to achieve maximum degradation of BS (85.6%). Moreover, the interactive effects of these parameters were investigated using three dimensional surface plots in terms of maximum fitness function. Importantly, it was concluded that the newly developed consortium is a potential candidate for biodegradation of BS in a safe, cost-effective and environmentally friendly manner.
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Affiliation(s)
- Fiaz Ahmad
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Samina Anwar
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Sadiqa Firdous
- Department of Microbiology, Women University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yin Da-Chuan
- Key Laboratory for Space Bioscience & Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Samina Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang Road, Faisalabad 38000, Pakistan.
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Ramadass M, Thiagarajan P. Effective pesticide nano formulations and their bacterial degradation. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1757-899x/263/2/022050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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