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Chen S, Liu C, Cao G, Li K, Huang J. Effect of salinity on biological nitrogen removal from wastewater and its mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:24713-24723. [PMID: 38499924 DOI: 10.1007/s11356-024-32417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
The nitrogen discharge from saline wastewater will cause significant pollution to the environment. As a high-efficiency and low-cost treatment method, biological treatment has a promising application prospect in the removal of nitrogen from high-salt wastewater. However, the inhibitory effect of high salt on microorganisms increases the difficulty of its treatment. This review discusses the influence of salinity on the nitrogen removal process, considering both traditional and novel biological techniques. Common methods to enhance the effectiveness of biological nitrogen removal processes and their mechanisms of action in engineering practice and research, including sludge acclimation and inoculation of halophilic bacteria, are also introduced. An outlook on the future development of biological nitrogen removal processes for high-salt wastewater is provided to achieve environmentally friendly discharge of high-salt wastewater.
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Affiliation(s)
- Shiqi Chen
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Cheng Liu
- College of Environment, Hohai University, Nanjing, 210098, China.
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, Hohai University, Nanjing, 210098, China.
| | - Guoxun Cao
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Ke Li
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Junliang Huang
- College of Environment, Hohai University, Nanjing, 210098, China
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Chavez Rodriguez L, Ingalls B, Schwarz E, Streck T, Uksa M, Pagel H. Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13638-13650. [PMID: 33064475 DOI: 10.1021/acs.est.0c03315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pesticides are widely used in agriculture despite their negative impact on ecosystems and human health. Biogeochemical modeling facilitates the mechanistic understanding of microbial controls on pesticide turnover in soils. We propose to inform models of coupled microbial dynamics and pesticide turnover with measurements of the abundance and expression of functional genes. To assess the advantages of informing models with genetic data, we developed a novel "gene-centric" model and compared model variants of differing structural complexity against a standard biomass-based model. The models were calibrated and validated using data from two batch experiments in which the degradation of the pesticides dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA) were observed in soil. When calibrating against data on pesticide mineralization, the gene-centric and biomass-based models performed equally well. However, accounting for pesticide-triggered gene regulation allows improved performance in capturing microbial dynamics and in predicting pesticide mineralization. This novel modeling approach also reveals a hysteretic relationship between pesticide degradation rates and gene expression, implying that the biodegradation performance in soils cannot be directly assessed by measuring the expression of functional genes. Our gene-centric model provides an effective approach for exploiting molecular biology data to simulate pesticide degradation in soils.
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Affiliation(s)
- Luciana Chavez Rodriguez
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada
| | - Erik Schwarz
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Marie Uksa
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany
| | - Holger Pagel
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
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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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Su X, Wang Y, Xue B, Zhang Y, Mei R, Zhang Y, Hashmi MZ, Lin H, Chen J, Sun F. Resuscitation of functional bacterial community for enhancing biodegradation of phenol under high salinity conditions based on Rpf. BIORESOURCE TECHNOLOGY 2018; 261:394-402. [PMID: 29684869 DOI: 10.1016/j.biortech.2018.04.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/08/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This study assumed that key degraders of functional bacterial community were prone to enter into the viable but non-culturable (VBNC) state under high saline phenolic conditions, and resuscitation-promoting factor (Rpf) could strengthen these degraders for better performances. Based on these assumptions, Rpf was used to enhance salt-tolerant phenol-degrading capability of functional populations in activated sludge. Results suggested that Rpf accelerated the start-up process during sludge domestication, and significantly enhanced salt-tolerant phenol-degrading capability. High-throughput sequencing showed that the resuscitation and stimulation functions of Rpf linked mainly to the genus Corynebacterium within the phylum Actinobacteria, and the genera Proteiniphilum and Petrimonas within the phylum Bacteroidete. These key functional populations contributed to better phenol-degrading capabilities under high salinity conditions. This study indicated that Rpf is a promising additive for improving biological treatment performance of saline phenolic wastewater.
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Affiliation(s)
- Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yuyang Wang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Binbing Xue
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yunge Zhang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Rongwu Mei
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou 310007, China
| | - Yu Zhang
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou 310007, China
| | - Muhammad Zaffar Hashmi
- Department of Meteorology, COMSATS Institute of Information Technology, Islamabad 44000, Pakistan
| | - Hongjun Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Jianrong Chen
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
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Wu X, Wang W, Liu J, Pan D, Tu X, Lv P, Wang Y, Cao H, Wang Y, Hua R. Rapid Biodegradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid by Cupriavidus gilardii T-1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3711-3720. [PMID: 28434228 DOI: 10.1021/acs.jafc.7b00544] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phytotoxicity and environmental pollution of residual herbicides have caused much public concern during the past several decades. An indigenous bacterial strain capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D), designated T-1, was isolated from soybean field soil and identified as Cupriavidus gilardii. Strain T-1 degraded 2,4-D 3.39 times more rapidly than the model strain Cupriavidus necator JMP134. T-1 could also efficiently degrade 2-methyl-4-chlorophenoxyacetic acid (MCPA), MCPA isooctyl ester, and 2-(2,4-dichlorophenoxy)propionic acid (2,4-DP). Suitable conditions for 2,4-D degradation were pH 7.0-9.0, 37-42 °C, and 4.0 mL of inoculums. Degradation of 2,4-D was concentration-dependent. 2,4-D was degraded to 2,4-dichlorophenol (2,4-DCP) by cleavage of the ether bond and then to 3,5-dichlorocatechol (3,5-DCC) via hydroxylation, followed by ortho-cleavage to cis-2-dichlorodiene lactone (CDL). The metabolites 2,4-DCP or 3,5-DCC at 10 mg L-1 were completely degraded within 16 h. Fast degradation of 2,4-D and its analogues highlights the potential for use of C. gilardii T-1 in bioremediation of phenoxyalkanoic acid herbicides.
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Affiliation(s)
- Xiangwei Wu
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Wenbo Wang
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Junwei Liu
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Dandan Pan
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Xiaohui Tu
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Pei Lv
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Yi Wang
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Haiqun Cao
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Yawen Wang
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
| | - Rimao Hua
- College of Resources and Environment, Key Laboratory of Agri-food Safety of Anhui Province, Anhui Agricultural University , Hefei 230036, People's Republic of China
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Tan S, Cui C, Hou Y, Chen X, Xu A, Li W, You H. Cultivation of activated sludge using sea mud as seed to treat industrial phenolic wastewater with high salinity. MARINE POLLUTION BULLETIN 2017; 114:867-870. [PMID: 27863884 DOI: 10.1016/j.marpolbul.2016.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 06/06/2023]
Abstract
A technique is proposed to treat saline hazardous wastewater by using marine activated sludge, cultivated with sea mud as seed. Since the developed marine activated sludge had phenol-tolerant microorganisms (MAS-1, MAS-2 and MAS-3) which originated from the ocean, it was envisaged that these bacteria could survive and breakdown phenol in saline environments. In this work, typical phenol-tolerant microorganisms were isolated from the marine activated sludge and identified. After a hierarchical acclimation process, the marine activated sludge was used to treat the industrial phenolic wastewater with high salinity. The marine activated sludge was able to break down phenol and other organic components effectively and efficiently in treating the wastewater with salinity of 5.7% w/v. The results showed a high removal of phenol (99%), COD (80%) and NH3-N (68%).
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Affiliation(s)
- Songwen Tan
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai 264209, China
| | - Chunzhi Cui
- Department of Chemistry, Yanbian University, Yanji 133002, China
| | - Yang Hou
- Department of Biological Science, Hunan Normal University, Changsha 410000, China
| | - Xuncai Chen
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney 2006, Australia
| | - Aiqin Xu
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai 264209, China
| | - Weiguo Li
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai 264209, China.
| | - Hong You
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai 264209, China
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Karami S, Maleki A, Karimi E, Poormazaheri H, Zandi S, Davari B, Salimi YZ, Gharibi F, Kalantar E. Biodegradation of 2,4-dichlorophenoxyacetic acid by bacteria with highly antibiotic-resistant pattern isolated from wheat field soils in Kurdistan, Iran. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:659. [PMID: 27832433 DOI: 10.1007/s10661-016-5673-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Recently, there has been increasing interest to clean up the soils contaminated with herbicide. Our aim was to determine the bioremediation of 2,4-dichlorophenoxyacetic acid (2,4-D) from wheat fields which have a long history of herbicide in Sanandaj. Based on our literature survey, this study is the first report to isolate and identify antimicrobial resistant bacteria from polluted wheat field soils in Sanandaj which has the capacity to degrade 2,4-D. From 150 2,4-D-exposed soil samples, five different bacteria were isolated and identified based on biochemical tests and 16S ribosomal RNA (rRNA). Pseudomonas has been the most frequently isolated genus. By sequencing the 16S rRNA gene of the isolated bacteria, the strains were detected and identified as a member of the genus Pseudomonas sp, Entrobacter sp, Bacillus sp, Seratia sp, and Staphylococcus sp. The sequence of Sanandaj 1 isolate displayed 87% similarity with the 16S rRNA gene of a Pseudomonas sp (HE995788). Similarly, all the isolates were compared to standard strains based on 16S rRNA. Small amounts of 2,4-D could be transmitted to a depth of 10-20 cm; however, in the depth of 20-40 cm, we could not detect the 2,4-D. The isolates were resistant to various antibiotics particularly, penicillin, ampicillin, and amoxicillin.
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Affiliation(s)
- Solmaz Karami
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
| | - Afshin Maleki
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
| | - Ebrahim Karimi
- Agriculture Biotechnology Research Institute of Iran, Karaj, Iran
| | - Helen Poormazaheri
- Dietary and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Shiva Zandi
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
| | - Behrooz Davari
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
- Department of Medical Entomology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Yahya Zand Salimi
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
| | - Fardin Gharibi
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran
| | - Enayatollah Kalantar
- Environmental Health Research Center, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran.
- Dietary and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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Tan S, Chen X, Cui C, Hou Y, Li W, You H. Biodegradation of saline phenolic wastewater in a biological contact oxidation reactor with immobilized cells of Oceanimonas sp. Biotechnol Lett 2016; 39:91-96. [PMID: 27659032 DOI: 10.1007/s10529-016-2226-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/13/2016] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To develop a method to treat saline phenolic wastewater in a biological contact oxidation reactor (BCOR) with immobilized cells of a marine microorganism, Oceanimonas sp., isolated from seawater. RESULTS Cells were immobilized on fibre carriers in the BCOR. Saline wastewater with phenol at 1.5 g/l and NaCl at 6 % (w/v) was treated. In continuous assays, 99 % removal of phenol was achieved and a kinetic model for the phenol degradation is presented based on Monod's equation. CONCLUSION The BOCR system using immobilized cells of Oceanimonas efficiently treats saline phenolic wastewaters without having decrease the salinity of the wastewater.
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Affiliation(s)
- Songwen Tan
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai, 264209, China
- Department of Chemistry, Yanbian University, Yanji, 133002, China
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Xuncai Chen
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Chunzhi Cui
- Department of Chemistry, Yanbian University, Yanji, 133002, China
| | - Yang Hou
- Department of Biological Science, Hunan Normal University, Changsha, 410000, China
| | - Weiguo Li
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai, 264209, China.
| | - Hong You
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai, 264209, China
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Chang YC, Reddy MV, Umemoto H, Sato Y, Kang MH, Yajima Y, Kikuchi S. Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques. PLoS One 2015; 10:e0145057. [PMID: 26710231 PMCID: PMC4699198 DOI: 10.1371/journal.pone.0145057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/29/2015] [Indexed: 11/21/2022] Open
Abstract
In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l-1) were carried out using CY-1. Effect of NaCl and KNO3 on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms.
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Affiliation(s)
- Young-Cheol Chang
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
- * E-mail:
| | - M. Venkateswar Reddy
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Honoka Umemoto
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Yuki Sato
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
| | - Mi-Hye Kang
- Seoul Metropolitan Government Research Institute of Public Health and Environment, 202–3 Yangjae-dong, Seocho-gu, Seoul, 137–893, Republic of Korea
| | - Yuka Yajima
- Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606–8501, Japan
| | - Shintaro Kikuchi
- Course of Chemical and Biological Engineering, Division of Sustainable and Environmental Engineering, College of Environmental Technology, Muroran Institute of Technology, 27–1 Mizumoto, Muroran, 050–8585, Japan
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Han L, Zhao D, Li C. Isolation and 2,4-D-degrading characteristics of Cupriavidus campinensis BJ71. Braz J Microbiol 2015; 46:433-41. [PMID: 26273258 PMCID: PMC4507535 DOI: 10.1590/s1517-838246220140211] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 10/30/2014] [Indexed: 11/22/2022] Open
Abstract
An indigenous bacterial strain capable of utilizing 2,4-dichlorophenoxyacetic acid as the sole carbon and energy source was isolated from a soil used for grown wheat with a long-term history of herbicide use in Beijing, China. The strain BJ71 was identified as Cupriavidus campinensis based on its 16S rRNA sequence analysis and morphological, physiological, and biochemical characteristics. The degradation characteristics of strain BJ71 were evaluated. The optimal conditions for 2,4-D degradation were as follows: pH 7.0, 30 °C, 3% (v/v) inoculum size, and an initial 2,4-D concentration of 350 mg L(-1). Up to 99.57% of the 2,4-D was degraded under optimal conditions after 6 days of incubation. Strain BJ71 was also able to degrade quizalofop and fluroxypyr. This is the first report of a 2,4-D-degrader containing tfdA gene that can utilize these two herbicides. In a biodegradation experiment, 87.13% and 42.53% of 2,4-D (initial concentration, 350 mg kg(-1)) was degraded in non-sterile and sterilized soil inoculated with BJ71, respectively, after 14 days. The 2,4-D degradation was more rapid in a soil microcosm including BJ71 than in a soil microcosm without BJ71. These results indicate that strain BJ71 is a potential candidate for the bioremediation of soil contaminated with the herbicide 2,4-D.
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Affiliation(s)
- Lizhen Han
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guiyang, China, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guiyang, China. ; Guizhou University, College of Life Sciences, Guizhou University, Guiyang, China, College of Life Sciences, Guizhou University, Guiyang, China. ; Guizhou University, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Degang Zhao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guiyang, China, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guiyang, China. ; Guizhou University, College of Life Sciences, Guizhou University, Guiyang, China, College of Life Sciences, Guizhou University, Guiyang, China. ; Guizhou University, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Cuicui Li
- Guizhou University, College of Life Sciences, Guizhou University, Guiyang, China, College of Life Sciences, Guizhou University, Guiyang, China. ; Guizhou University, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
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Han L, Liu Y, Li C, Zhao D. Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71. World J Microbiol Biotechnol 2015; 31:1021-30. [PMID: 25850533 DOI: 10.1007/s11274-015-1852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D)/α-ketoglutarate (α-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. Previous studies focused on the tfdA gene in Ralstonia eutropha JMP134 isolated in Australia. In this study, a new tfdA gene was cloned from Cupriavidus campinensis BJ71, an effective degrading bacteria from China, based on the iCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (iCODEHOPs) protocol, combined with high-efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR). The open reading frame of 861 bp encoded a putative 287 amino acid protein with a theoretical molecular mass of 32.32 kDa. The gene was overexpressed in Escherichia coli BL21 (DE3) and the purified TfdA showed optimal activity at pH 6.75 and 30 °C. This enzyme was more thermostable and it could use 3-hydrocinnamic acid as substrate, with a similar enzyme activity compared with 2,4-D. TfdA and its variants were created as maltose-binding protein (MBP) tagged fusion proteins to examine the roles of putative substrate-binding residues. The MBP-N110A, MBP-V198A and MBP-R207K proteins showed decreased k cat and increased Km, and MBP-R278A was inactive, suggesting these residues may affect 2,4-D binding or catalysis.
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Affiliation(s)
- Lizhen Han
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guiyang, 550025, China,
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16S rRNA gene phylogeny and tfdA gene analysis of 2,4-D-degrading bacteria isolated in China. World J Microbiol Biotechnol 2014; 30:2567-76. [PMID: 24898178 DOI: 10.1007/s11274-014-1680-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Twenty-two 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial isolates were collected from agricultural soils at three sites in China. Sequence analysis of the 16S rRNA genes indicated that the isolates were phylogenetically grouped into four categories: Ochrobactrum anthropi, in the Alpha- class of the phylum Proteobacteria (3 out of 22 isolates), Cupriavidus sp., of the Betaproteobacteria (3 out of 22), Pseudomonas sp. and Stenotrophomonas sp., which are Gammaproteobacteria (7 out of 22), and Bacillus sp., of the phylum Firmicutes (9 out of 22). Primers were designed to amplify the conserved domain of tfdA, which is known to be involved in the degradation of 2,4-D. Results showed that the tfdA genes of all 22 strains were most similar to that of Cupriavidus necator JMP134, which belongs to the 2,4-D/α-ketoglutarate dioxygenase TfdA protein family, indicating that the JMP134-type tfdA gene is likely to be almost universal among the 2,4-D-degrading bacteria isolated from China. Degradation abilities of these 22 strains were investigated in assays using 2,4-D as the sole source of carbon and energy. Thirteen strains degraded >60 % of the available 2,4-D (500 mg l(-1)) over a 1-week incubation period, while a further nine Bacillus sp. strains degraded 50-81 % of the available 2,4-D. None of these nine strains degraded other selected herbicides, such as mecoprop, 2-methyl-4-chlorophenoxyacetic acid, quizalofop, and fluroxypyr. This is the first report of 2,4-D-degradation by Bacilli.
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Zabaloy MC, Gómez MA. Isolation and characterization of indigenous 2,4-D herbicide degrading bacteria from an agricultural soil in proximity of Sauce Grande River, Argentina. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0731-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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14
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Modeling of phenoxy acid herbicide mineralization and growth of microbial degraders in 15 soils monitored by quantitative real-time PCR of the functional tfdA gene. Appl Environ Microbiol 2012; 78:5305-12. [PMID: 22635998 DOI: 10.1128/aem.00990-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of tfdA in the range 1 × 10(5) to 5 × 10(7) gene copies g(-1) of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model.
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Zaprasis A, Liu YJ, Liu SJ, Drake HL, Horn MA. Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil. Appl Environ Microbiol 2010; 76:119-28. [PMID: 19880651 PMCID: PMC2798625 DOI: 10.1128/aem.01727-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 10/20/2009] [Indexed: 11/20/2022] Open
Abstract
Phenoxyalkanoic acid (PAA) herbicides are widely used in agriculture. Biotic degradation of such herbicides occurs in soils and is initiated by alpha-ketoglutarate- and Fe2+-dependent dioxygenases encoded by tfdA-like genes (i.e., tfdA and tfdAalpha). Novel primers and quantitative kinetic PCR (qPCR) assays were developed to analyze the diversity and abundance of tfdA-like genes in soil. Five primer sets targeting tfdA-like genes were designed and evaluated. Primer sets 3 to 5 specifically amplified tfdA-like genes from soil, and a total of 437 sequences were retrieved. Coverages of gene libraries were 62 to 100%, up to 122 genotypes were detected, and up to 389 genotypes were predicted to occur in the gene libraries as indicated by the richness estimator Chao1. Phylogenetic analysis of in silico-translated tfdA-like genes indicated that soil tfdA-like genes were related to those of group 2 and 3 Bradyrhizobium spp., Sphingomonas spp., and uncultured soil bacteria. Soil-derived tfdA-like genes were assigned to 11 clusters, 4 of which were composed of novel sequences from this study, indicating that soil harbors novel and diverse tfdA-like genes. Correlation analysis of 16S rRNA and tfdA-like gene similarity indicated that any two bacteria with D>20% of group 2 tfdA-like gene-derived protein sequences belong to different species. Thus, data indicate that the soil analyzed harbors at least 48 novel bacterial species containing group 2 tfdA-like genes. Novel qPCR assays were established to quantify such new tfdA-like genes. Copy numbers of tfdA-like genes were 1.0x10(6) to 65x10(6) per gram (dry weight) soil in four different soils, indicating that hitherto-unknown, diverse tfdA-like genes are abundant in soils.
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Affiliation(s)
- Adrienne Zaprasis
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440 Bayreuth, Germany, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ya-Jun Liu
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440 Bayreuth, Germany, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Shuang-Jiang Liu
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440 Bayreuth, Germany, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440 Bayreuth, Germany, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440 Bayreuth, Germany, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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TaqMan probe-based real-time PCR assay for detection and discrimination of class I, II, and III tfdA genes in soils treated with phenoxy acid herbicides. Appl Environ Microbiol 2009; 75:2969-72. [PMID: 19251892 DOI: 10.1128/aem.02051-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Separate quantification of three classes of tfdA genes was performed using TaqMan quantitative real-time PCR for 13 different soils subsequent to mineralization of three phenoxy acids. Class III tfdA genes were found to be involved in mineralization more often than class I and II tfdA genes.
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Huong NL, Itoh K, Suyama K. 2,4-Dichlorophenoxyacetic Acid (2,4-D)- and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacterial Community in Soil-Water Suspension during the Enrichment Process. Microbes Environ 2008; 23:142-8. [DOI: 10.1264/jsme2.23.142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nguyen L. Huong
- Faculty of Life and Environmental Science, Shimane University
| | - Kazuhito Itoh
- Faculty of Life and Environmental Science, Shimane University
| | - Kousuke Suyama
- Faculty of Life and Environmental Science, Shimane University
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Morono Y, Kitagawa W, Kimura N, Noda N, Nakamura K, Kamagata Y. “Mark the Gene”: a Method for Nondestructive Introduction of Marker Sequences Inside the Gene Frame of Transgenes. Appl Environ Microbiol 2007; 73:4915-21. [PMID: 17526781 PMCID: PMC1951010 DOI: 10.1128/aem.00068-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
A specific marking and detection technique is a fundamental requirement for the safer use of genetically modified (GM) organisms. Here we propose a simple and effective method for directly marking functional transgenes in GM organisms. For that purpose, we introduced nucleotide substitutions (NS), based on the degeneracy of codons as markers (NS markers), into the
bphC
(2,3-dihydroxybiphenyl dioxygenase) and
tomA3
(toluene-
ortho
-monooxygenase) gene frames using a PCR-based method. No change was observed in the enzyme activity of translated proteins, and alignments with homologous genes showed the uniqueness of the NS markers. Furthermore, we constructed
tomA3
variations harboring NS markers in different positions. Although the translational products were identical, the constructed variation genes could be distinguished through their marker patterns by multiplex PCR, showing that NS markers could serve as product-specific tags for identifying individual GM organisms. This direct method of marking the functional transgene provides a simple, low-risk, and robust marking method without causing the gene functions to deteriorate.
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Affiliation(s)
- Yuki Morono
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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Spain AM, Peacock AD, Istok JD, Elshahed MS, Najar FZ, Roe BA, White DC, Krumholz LR. Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer. Appl Environ Microbiol 2007; 73:4892-904. [PMID: 17557842 PMCID: PMC1951013 DOI: 10.1128/aem.00331-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 05/30/2007] [Indexed: 02/01/2023] Open
Abstract
Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.
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Affiliation(s)
- Anne M Spain
- University of Oklahoma, Department of Botany and Microbiology, Norman, OK 73019, USA
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Sakai Y, Ogawa N, Fujii T, Sugahara K, Miyashita K, Hasebe A. 2,4-Dichrolophenoxyacetic Acid-degrading Genes from Bacteria Isolated from Soil in Japan: Spread of Burkholderia cepacia RASC-type Degrading Genes Harbored on Large Plasmids. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yoriko Sakai
- National Institute for Agro-Environmental Sciences
| | - Naoto Ogawa
- National Institute for Agro-Environmental Sciences
| | | | | | | | - Akira Hasebe
- National Institute for Agro-Environmental Sciences
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21
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Suyama T, Matsuura N, Kanagawa T. A proportional analysis method using non-kinetic real-time PCR. J Biotechnol 2006; 128:41-9. [PMID: 17079044 DOI: 10.1016/j.jbiotec.2006.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/07/2006] [Accepted: 09/21/2006] [Indexed: 01/19/2023]
Abstract
Prompted by increasing interest in proportional analysis of genetic types, we developed a simple assay technique for determining the ratio of a specific target gene in the total genes that can be amplified with the same PCR primer. The key feature of this method is that the following two tasks are performed in a single-tube real-time PCR system: task 1, PCR amplification of the total genes including the target using a labeled PCR primer, with concurrent monitoring of the total copy number of the PCR product; task 2, detection of the signal of the target gene at each cycle of amplification, using a labeled nucleotide probe. In principle, the ratio of the target gene to the total genes is represented by the signal detected in 'task 2' at the cycle in which the PCR product reached a prescribed copy number (assessed by 'task 1').
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Affiliation(s)
- Tetsushi Suyama
- National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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Baelum J, Henriksen T, Hansen HCB, Jacobsen CS. Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene. Appl Environ Microbiol 2006; 72:1476-86. [PMID: 16461702 PMCID: PMC1392919 DOI: 10.1128/aem.72.2.1476-1486.2006] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tfdA gene is known to be involved in the first step of the degradation of the phenoxy acid herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in several soil bacteria, but bacteria containing other tfdA-like genes have been isolated as well. A quantitative real-time PCR method was used to monitor the increase in the concentration of tfdA genes during degradation of MCPA in sandy topsoil and subsoil over a period of 115 days. Quantitative PCR revealed growth in the tfdA-containing bacterial community, from 500 genes g(-1) soil to approximately 3 x 10(4) genes g(-1) soil and to 7 x 10(5) genes g(-1) soil for topsoil initially added to 2.3 mg MCPA kg(-1) (dry weight) soil and 20 mg MCPA kg(-1) (dry weight) soil, respectively. We analyzed the diversity of the tfdA gene during the degradation experiment. Analyses of melting curves of real-time PCR amplification products showed that a shift in the dominant tfdA population structure occurred during the degradation period. Further denaturing gradient gel electrophoresis and sequence analysis revealed that the tfdA genes responsible for the degradation of MCPA belonged to the class III tfdA genes, while the tfdA genes present in the soil before the occurrence of degradation belonged to the class I tfdA genes. The implications of these results is that the initial assessment of functional genes in soils does not necessarily reflect the organisms or genes that would carry out the degradation of the compounds in question.
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Affiliation(s)
- Jacob Baelum
- Department of Geochemistry, Geological Survey of Denmark and Greenland, Øster Voldgade 10, DK-1350 Copenhagen K, Denmark
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23
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Affiliation(s)
- Yoichi Kamagata
- Institute for Biological Resources & Functions, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Hideyuki Tamaki
- Institute for Biological Resources & Functions, National Institute of Advanced Industrial Science and Technology (AIST)
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