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Sun M, Xu W, Zhang W, Guang C, Mu W. Microbial elimination of carbamate pesticides: specific strains and promising enzymes. Appl Microbiol Biotechnol 2022; 106:5973-5986. [PMID: 36063179 DOI: 10.1007/s00253-022-12141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
Carbamate pesticides are widely used in the environment, and compared with other pesticides in nature, they are easier to decompose and have less durability. However, due to the improper use of carbamate pesticides, some nontarget organisms still may be harmed. To this end, it is necessary to investigate effective removal or elimination methods for carbamate pesticides. Current effective elimination methods could be divided into four categories: physical removal, chemical reaction, biological degradation, and enzymatic degradation. Physical removal primarily includes elution, adsorption, and supercritical fluid extraction. The chemical reaction includes Fenton oxidation, photo-radiation, and net electron reduction. Biological degradation is an environmental-friendly manner, which achieves degradation by the metabolism of microorganisms. Enzymatic degradation is more promising due to its high substrate specificity and catalytic efficacy. All in all, this review primarily summarizes the property of carbamate pesticides and the traditional degradation methods as well as the promising biological elimination. KEY POINTS: • The occurrence and toxicity of carbamate pesticides were shown. • Biological degradation strains against carbamate pesticides were presented. • Promising enzymes responsible for the degradation of carbamates were discussed.
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Affiliation(s)
- Minwen Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
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Two LysR family transcriptional regulators, McbH and McbN, activate the operons responsible for the midstream and downstream pathways of carbaryl degradation in Pseudomonas sp. strain XWY-1, respectively. Appl Environ Microbiol 2021; 88:e0206021. [PMID: 34936841 DOI: 10.1128/aem.02060-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, a LysR family transcriptional regulator McbG that activates the mcbBCDEF gene cluster involved in the upstream pathway (from carbaryl to salicylate) of carbaryl degradation in Pseudomonas sp. strain XWY-1 has been identified by us (Appl. Environ. Microbiol. 2021, 87(9): e02970-20.). In this study, we identified McbH and McbN, which activate mcbIJKLM cluster (responsible for the midstream pathway, from salicylate to gentisate) and mcbOPQ cluster (responsible for the downstream pathway, from gentisate to pyruvate and fumarate), respectively. They both belong to the LysR family of transcriptional regulators. Gene disruption and complementation study reveal that McbH is essential for transcription of the mcbIJKLM cluster in response to salicylate and McbN is indispensable for the transcription of the mcbOPQ cluster in response to gentisate. The results of electrophoretic mobility shift assay (EMSA) and DNase I footprinting showed that McbH binds to the 52-bp motif in the mcbIJKLM promoter area and McbN binds to the 58-bp motif in the mcbOPQ promoter area. The key sequence of McbH binding to mcbIJKLM promoter is a 13-bp motif that conforms to the typical characteristics of LysR family. However, the 12-bp motif that is different from the typical characteristics of the LysR family regulator binding site sequence is identified as the key sequence for McbN to bind to the mcbOPQ promoter. This study reveals the regulatory mechanism for the midstream and downstream pathway of carbaryl degradation in strain XWY-1 and further enriches the members of the LysR transcription regulator family. IMPORTANCE: The enzyme-encoding genes involved in the complete degradation pathway of carbaryl in Pseudomonas sp. strain XWY-1 include mcbABCDEF, mcbIJKLM and mcbOPQ. Previous studies demonstrated that the mcbA gene responsible for hydrolysis of carbaryl to 1-naphthol is constitutively expressed and the transcription of mcbBCDEF was regulated by McbG. However, the transcription regulation mechanisms of mcbIJKLM and mcbOPQ have not been investigated yet. In this study, we identified two LysR-type transcriptional regulators, McbH and McbN, which activate the mcbIJKLM cluster responsible for the degradation of salicylate to gentisate and mcbOPQ cluster responsible for the degradation of gentisate to pyruvate and fumarate, respectively. The 13-bp motif is critical for McbH to bind to the promoter of mcbIJKLM, and 12-bp motif different from the typical characteristics of the LTTR binding sequence affects the binding of McbN to promoter. These findings help to expand the understanding of the regulatory mechanism of microbial degradation of carbaryl.
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Ke Z, Zhu Q, Jiang W, Zhou Y, Zhang M, Jiang M, Hong Q. Heterologous expression and exploration of the enzymatic properties of the carbaryl hydrolase CarH from a newly isolated carbaryl-degrading strain. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112666. [PMID: 34416635 DOI: 10.1016/j.ecoenv.2021.112666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Carbaryl is the representative of carbamate insecticide. As an acetylcholinesterase inhibitor, it poses potential threat to humans and other non-target organisms. Agrobacterium sp. XWY-2, which could grow with carbaryl as the sole carbon source, was isolated and characterized. The carH gene, encoding a carbaryl hydrolase, was cloned from strain XWY-2 and expressed in Escherichia coli BL21 (DE3). CarH was able to hydrolyze carbamate pesticides including carbaryl, carbofuran, isoprocarb, propoxur and fenobucarb efficiently, while it hydrolyzed oxamyl and aldicarb poorly. The optimal pH of CarH was 8.0 and the optimal temperature was 30 ℃. The apparent Km and kcat values of CarH for carbaryl were 38.01 ± 2.81 μM and 0.33 ± 0.01 s-1, respectively. The point mutation experiment demonstrated that His341, His343, His346, His416 and D437 are the key sites for CarH to hydrolyze carbaryl.
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Affiliation(s)
- Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qian Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Mingli Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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McbG, a LysR Family Transcriptional Regulator, Activates the mcbBCDEF Gene Cluster Involved in the Upstream Pathway of Carbaryl Degradation in Pseudomonas sp. Strain XWY-1. Appl Environ Microbiol 2021; 87:AEM.02970-20. [PMID: 33579686 DOI: 10.1128/aem.02970-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/06/2021] [Indexed: 11/20/2022] Open
Abstract
Although enzyme-encoding genes involved in the degradation of carbaryl have been reported in Pseudomonas sp. strain XWY-1, no regulator has been identified yet. In the mcbABCDEF cluster responsible for the upstream pathway of carbaryl degradation (from carbaryl to salicylate), the mcbA gene is constitutively expressed, while mcbBCDEF is induced by 1-naphthol, the hydrolysis product of carbaryl by McbA. In this study, we identified McbG, a transcriptional activator of the mcbBCDEF cluster. McbG is a 315-amino-acid protein with a molecular mass of 35.7 kDa. It belongs to the LysR family of transcriptional regulators and shows 28.48% identity to the pentachlorophenol (PCP) degradation transcriptional activation protein PcpR from Sphingobium chlorophenolicum ATCC 39723. Gene disruption and complementation studies reveal that mcbG is essential for transcription of the mcbBCDEF cluster in response to 1-naphthol in strain XWY-1. The results of the electrophoretic mobility shift assay (EMSA) and DNase I footprinting show that McbG binds to the 25-bp motif in the mcbBCDEF promoter area. The palindromic sequence TATCGATA within the motif is essential for McbG binding. The binding site is located between the -10 box and the transcription start site. In addition, McbG can repress its own transcription. The EMSA results show that a 25-bp motif in the mcbG promoter area plays an important role in McbG binding to the promoter of mcbG This study reveals the regulatory mechanism for the upstream pathway of carbaryl degradation in strain XWY-1. The identification of McbG increases the variety of regulatory models within the LysR family of transcriptional regulators.IMPORTANCE Pseudomonas sp. strain XWY-1 is a carbaryl-degrading strain that utilizes carbaryl as the sole carbon and energy source for growth. The functional genes involved in the degradation of carbaryl have already been reported. However, the regulatory mechanism has not been investigated yet. Previous studies demonstrated that the mcbA gene, responsible for hydrolysis of carbaryl to 1-naphthol, is constitutively expressed in strain XWY-1. In this study, we identified a LysR-type transcriptional regulator, McbG, which activates the mcbBCDEF gene cluster responsible for the degradation of 1-naphthol to salicylate and represses its own transcription. The DNA binding site of McbG in the mcbBCDEF promoter area contains a palindromic sequence, which affects the binding of McbG to DNA. These findings enhance our understanding of the mechanism of microbial degradation of carbaryl.
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Zhou Y, Ke Z, Ye H, Hong M, Xu Y, Zhang M, Jiang W, Hong Q. Hydrolase CehA and a Novel Two-Component 1-Naphthol Hydroxylase CehC1C2 are Responsible for the Two Initial Steps of Carbaryl Degradation in Rhizobium sp. X9. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14739-14747. [PMID: 33264024 DOI: 10.1021/acs.jafc.0c03845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Carbaryl is a widely used carbamate pesticide in agriculture. The strain Rhizobium sp. X9 possesses the typical carbaryl degradation pathway in which carbaryl is mineralized via 1-naphthol, salicylate, and gentisate. In this study, we cloned a carbaryl hydrolase gene cehA and a novel two-component 1-naphthol hydroxylase gene cehC1C2. CehA mediates carbaryl hydrolysis to 1-naphthol and CehC1, an FMNH2 or FADH2-dependent monooxygenase belonging to the HpaB superfamily, and hydroxylates 1-naphthol in the presence of reduced nicotinamide-adenine dinucleotide (FMN)/flavin adenine dinucleotide (FAD), and the reductase CehC2. CehC1 has the highest amino acid similarity (58%) with the oxygenase component of a two-component 4-nitrophenol 2-monooxygenase, while CehC2 has the highest amino acid similarity (46%) with its reductase component. CehC1C2 could utilize both FAD and FMN as the cofactor during the hydroxylation, although higher catalytic activity was observed with FAD as the cofactor. The optimal molar ratio of CehC1 to CehC2 was 2:1. The Km and Kcat/Km values of CehC1 for 1-naphthol were 74.71 ± 16.07 μM and (8.29 ± 2.44) × 10-4 s-1·μM-1, respectively. Moreover, the enzyme activities and substrate spectrum between CehC1C2 and previously reported 1-naphthol hydroxylase McbC were compared. The results suggested that McbC had a higher 1-naphthol hydroxylation activity, while CehC1C2 had a broader substrate spectrum.
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Affiliation(s)
- Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Hangting Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Mengting Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Yifei Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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Qin D, Ma C, Lv M, Yu CP. Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:1822-1829. [PMID: 32048985 DOI: 10.1099/ijsem.0.003978] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXBT, capable of degrading estrogens, and another, YL23T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25-35 °C and pH 7.0-8.0. While strain AXBT could tolerate 3 % (w/v) NaCl, YL23T could only grow between 0-1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c) as the major fatty acids and diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G+C contents of strains AXBT and YL23T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXBT and YL23T belonged to the genus Sphingobium. Strain AXBT was most closely related to Sphingobium chlorophenolicum NBRC 16172T (97.5 %) and Sphingobium chungbukense DJ77T (97.2 %), and strain YL23T was most closely related to S. chlorophenolicum NBRC 16172T (97.4 %) and S. quisquiliarum P25T (97.1 %). Average nucleotide identity values between these two strains and S. chlorophenolicum NBRC 16172T, S. chungbukense DJ77T, Sphingobium chinhatense IP26T, Sphingobium quisquiliarum P25T and Sphingobium japonicum UT26ST were from 80.7 to 85.8 %. In conclusion, strains AXBT and YL23T represent novel species of the genus Sphingobium, for which the names Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov. are proposed, respectively. The type strains of S. estronivorans and S. bisphenolivorans are AXBT (=MCCC 1K01232T=DSM 102173T) and YL23T (=MCCC 1K02300T=DSM 102172T), respectively.
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Affiliation(s)
- Dan Qin
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China
| | - Cong Ma
- Xiamen Water Environment Technology Co., Ltd, Xiamen, Fujian 361000, PR China
| | - Min Lv
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Chang-Ping Yu
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC.,CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China
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8
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Kaur P, Balomajumder C. Simultaneous biodegradation of mixture of carbamates by newly isolated Ascochyta sp. CBS 237.37. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:590-599. [PMID: 30476821 DOI: 10.1016/j.ecoenv.2018.11.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
In this study, a mixture of carbamates (CRBs) degrading Carb.1b strain was isolated from soil. Based on the morphology and 18S rRNA sequence analysis, the strain was identified as an Ascochyta sp. CBS 237.37 with accession number MG786925. The isolate was employed in two growth mediums (added carbon and carbon-free) enriched with varied concentrations of CRBs ranging from 25 to 85 mg L-1 to assess its degradation efficacy. As determined by the Response Surface Methodology (RSM), optimum parameters for the degradation were: pH value of 7.5 and temperature of 28 °C. The degradation was inhibited at higher concentrations and was found to be 91.2%/94.8%, 67.25%/71.75%, 55.81%/59.81%, 46.85%/49.57% and 36%/40.80% (in carbon-free/added carbon) after 20 d. The removal of the higher concentration CRBs was comparatively slower, and the obtained degradation rate constant (Kavg) 0.03412 d-1. Added carbon and carbon-free medium removed over 86.7%/90.15% of CRBs (85 mgL-1) with the half-life (t1/2) of 26 d and R2 ranging from 0.982 to 0.999; indicating the high tolerance of carb.1b strain towards CRBs. Residual analysis of CRBs biodegradation was performed using GC/MS analysis. This is the first report of degradation of a mixture of CRBs by Ascochyta sp. CBS 237.37. The results of this study can possibly impact the development strategies of bioremediation for the elimination of CRBs.
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Affiliation(s)
- Parminder Kaur
- Department of Chemical Engineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| | - Chandrajit Balomajumder
- Department of Chemical Engineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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Aroua I, Abid G, Souissi F, Mannai K, Nebli H, Hattab S, Borgi Z, Jebara M. Identification of two pesticide-tolerant bacteria isolated from Medicago sativa nodule useful for organic soil phytostabilization. Int Microbiol 2018; 22:111-120. [PMID: 30810937 DOI: 10.1007/s10123-018-0033-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
Plant-microbe interactions such as rhizobacteria legumes are interesting in organic farming that has undergone significant expansion in the world. The organic agriculture is as an environment-friendly technique and a sustainable alternative to intensive agricultural system. Three types of soil were chosen, organic (ORG), conventional (CON), and fallow land (NA) to isolate soil bacteria-nodulating Medicago sativa, in order to develop microbial inoculants for use in agricultural sustainable system. Soil analysis revealed significant higher amounts of total nitrogen, organic carbon, total phosphorus, and matter detected in ORG. As for heavy metals, ORG showed high Cu content due to the authorized chemical use in organic farming. A sample of 130 bacteria was isolated from Medicago sativa nodule, genetically characterized by PCR/RFLP of ribosomal 16S RNAs, and a great dominance of Sinorhizobium meliloti (88.4%, 73.8%, and 55.5%) is obtained among NA-, CON-, and ORG-managed soils, respectively. The ORG showed the high bacterial diversity with 13.3% of non-identified strains. The resistance against five pesticides (Prosper, Cuivox, Fungastop, Nimbecidine, and Maneb) revealed a maximum of inhibitory concentration about 10 mg l-1 of Prosper, 12 mg l-1 of Cuivox, 6 ml l-1 of Fungastop, 7.5 ml l-1of Nimbecidine, and 25 ml l-1 of Maneb. The analysis of the symbiotic properties and plant growth-promoting potential revealed two efficient strains significantly increased alfalfa dry weight through producing siderophores, phosphorus, and indole acetic acid (13.6 mg ml-1 and 19.9 mg ml-1 respectively). Hence, we identify two tolerant and efficient strains, Achromobacter spanium and Serratia plymuthica, isolated from Medicago sativa nodule with valuable potential able to phytostabilize pesticide-contaminated soils.
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Affiliation(s)
- Ibtissem Aroua
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Ghassen Abid
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Fatma Souissi
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Khdiri Mannai
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia
| | - Houcem Nebli
- The Technical Center of Organic Agriculture in Chott Meriem, BP 54, 4042, Chott Meriem, Sousse, Tunisia
| | - Sabrine Hattab
- The Regional Center of Research in Horticulture and Organic Agriculture in Chott-Meriem Route Touristique, 4042, Chott Meriem, Tunisia
| | - Ziad Borgi
- The Technical Center of Organic Agriculture in Chott Meriem, BP 54, 4042, Chott Meriem, Sousse, Tunisia
| | - Moez Jebara
- Center of Biotechnology of Borj Cedria, Laboratory of Legumes, University of Carthage, BP 901, 2050, Hammam Lif, Tunisia.
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Selvarajan R, Sibanda T, Venkatachalam S, Kamika I, Nel WAJ. Industrial wastewaters harbor a unique diversity of bacterial communities revealed by high-throughput amplicon analysis. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1349-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Zhu S, Qiu J, Wang H, Wang X, Jin W, Zhang Y, Zhang C, Hu G, He J, Hong Q. Cloning and expression of the carbaryl hydrolase gene mcbA and the identification of a key amino acid necessary for carbaryl hydrolysis. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:1126-1135. [PMID: 30216972 DOI: 10.1016/j.jhazmat.2017.12.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/13/2017] [Accepted: 12/03/2017] [Indexed: 06/08/2023]
Abstract
Carbamate hydrolase is the initial and key enzyme for degradation of carbamate pesticides. In the present study, we report the isolation of a carbaryl-degrading strain Pseudomonas sp. XWY-1, the cloning of its carbaryl hydrolase gene (mcbA) and the characterization of McbA. Strain XWY-1 was able to utilize carbaryl as a sole carbon source and degrade it using 1-naphthol as an intermediate. Transposon mutagenesis identified a mutant of XWY-1M that was unable to hydrolyze carbaryl. The transposon-disrupted gene mcbA was cloned by self-formed adaptor PCR, then expressed in Escherichia coli BL21(DE3) and purified. McbA was able to hydrolyze carbamate pesticides including carbaryl, isoprocarb, fenobucarb, carbofuran efficiently, while it hydrolyzed aldicarb, and propoxur poorly. The optimal pH of McbA was 7.0 and the optimal temperature was 40°C. The apparent Km and kcat values of McbA for carbaryl were 77.67±12.31μM and 2.12±0.10s-1, respectively. Three amino acid residues (His467, His477 and His504) in the predicted polymerase/histidinol phosphatase-like domain were shown to be closely related to the activity of McbA, with His504 being the most important, as a replacement of His504 led to the complete loss of activity. This is the first study to identify key amino acids in McbA.
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Affiliation(s)
- Shijun Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiang Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Wen Jin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yingkun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Chenfei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Gang Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China; Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Sun L, Liu H, Gao X, Chen W, Huang K, Zhang S. Isolation of monocrotophos-degrading strain Sphingobiumsp. YW16 and cloning of its TnopdA. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4942-4950. [PMID: 29204940 DOI: 10.1007/s11356-017-0718-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
The bacterial strain Sphingobium sp. YW16, which is capable of degrading monocrotophos, was isolated from paddy soil in China. Strain YW16 could hydrolyze monocrotophos to dimethylphosphate and N-methylacetoacetamide and utilize dimethylphosphate as the sole carbon source but could not utilize N-methylacetoacetamide. Strain YW16 also had the ability to hydrolyze other organophosphate pesticides. A fragment (7067 bp) that included the organophosphorus hydrolase gene, opdA, was acquired from strain YW16 using the shotgun technique combined with SEFA-PCR. Its sequence illustrated that opdA was included in TnopdA, which consisted of a transpose gene, a putative integrase gene, a putative ATP-binding protein gene, and opdA. Additionally, a conjugal transfer protein gene, traI, was located downstream of TnopdA. The juxtaposition of TnopdA with TraI suggests that opdA may be transferred from strain YW16 to other bacteria through conjugation. OpdA was able to hydrolyze a wide range of organophosphate pesticides, with the hydrolysis efficiency decreasing as follows: methyl parathion > fenitrothion > phoxim > dichlorvos > ethyl parathion > trichlorfon > triazophos > chlorpyrifos > monocrotophos > diazinon. This work provides the first report of opdA in the genus Sphingobium.
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Affiliation(s)
- Lina Sun
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, People's Republic of China
| | - Hongming Liu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, Wuhu, 241000, People's Republic of China
| | - Xinhua Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, People's Republic of China
| | - Wei Chen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, People's Republic of China
| | - Kaihua Huang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China
- Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, People's Republic of China
| | - Sui Zhang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, People's Republic of China.
- Shanghai Engineering Research Center of Low-carbon Agriculture (SERCLA), Shanghai, 201403, People's Republic of China.
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Compartmentalization of the Carbaryl Degradation Pathway: Molecular Characterization of Inducible Periplasmic Carbaryl Hydrolase from Pseudomonas spp. Appl Environ Microbiol 2018; 84:AEM.02115-17. [PMID: 29079626 DOI: 10.1128/aem.02115-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/24/2017] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas sp. strains C5pp and C7 degrade carbaryl as the sole carbon source. Carbaryl hydrolase (CH) catalyzes the hydrolysis of carbaryl to 1-naphthol and methylamine. Bioinformatic analysis of mcbA, encoding CH, in C5pp predicted it to have a transmembrane domain (Tmd) and a signal peptide (Sp). In these isolates, the activity of CH was found to be 4- to 6-fold higher in the periplasm than in the cytoplasm. The recombinant CH (rCH) showed 4-fold-higher activity in the periplasm of Escherichia coli The deletion of Tmd showed activity in the cytoplasmic fraction, while deletion of both Tmd and Sp (Tmd+Sp) resulted in expression of the inactive protein. Confocal microscopic analysis of E. coli expressing a (Tmd+Sp)-green fluorescent protein (GFP) fusion protein revealed the localization of GFP into the periplasm. Altogether, these results indicate that Tmd probably helps in anchoring of polypeptide to the inner membrane, while Sp assists folding and release of CH in the periplasm. The N-terminal sequence of the mature periplasmic CH confirms the absence of the Tmd+Sp region and confirms the signal peptidase cleavage site as Ala-Leu-Ala. CH purified from strains C5pp, C7, and rCHΔ(Tmd)a were found to be monomeric with molecular mass of ∼68 to 76 kDa and to catalyze hydrolysis of the ester bond with an apparent Km and Vmax in the range of 98 to 111 μM and 69 to 73 μmol · min-1 · mg-1, respectively. The presence of low-affinity CH in the periplasm and 1-naphthol-metabolizing enzymes in the cytoplasm of Pseudomonas spp. suggests the compartmentalization of the metabolic pathway as a strategy for efficient degradation of carbaryl at higher concentrations without cellular toxicity of 1-naphthol.IMPORTANCE Proteins in the periplasmic space of bacteria play an important role in various cellular processes, such as solute transport, nutrient binding, antibiotic resistance, substrate hydrolysis, and detoxification of xenobiotics. Carbaryl is one of the most widely used carbamate pesticides. Carbaryl hydrolase (CH), the first enzyme of the degradation pathway which converts carbaryl to 1-naphthol, was found to be localized in the periplasm of Pseudomonas spp. Predicted transmembrane domain and signal peptide sequences of Pseudomonas were found to be functional in Escherichia coli and to translocate CH and GFP into the periplasm. The localization of low-affinity CH into the periplasm indicates controlled formation of toxic and recalcitrant 1-naphthol, thus minimizing its accumulation and interaction with various cellular components and thereby reducing the cellular toxicity. This study highlights the significance of compartmentalization of metabolic pathway enzymes for efficient removal of toxic compounds.
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Draft Genome Sequence of the Type Strain Sphingopyxis bauzanensis DSM 22271. GENOME ANNOUNCEMENTS 2017; 5:5/37/e01014-17. [PMID: 28912333 PMCID: PMC5597774 DOI: 10.1128/genomea.01014-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here the draft genome sequence of Sphingopyxis bauzanensis DSM 22271. The assembly contains 4,258,005 bp in 28 scaffolds and has a GC content of 63.3%. A series of specific genes involved in the catabolism or transport of aromatic compounds was identified.
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15
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Du J, Singh H, Yang JE, Yin CS, Kook M, Yu H, Yi TH. Sphingobium soli sp. nov. isolated from rhizosphere soil of a rose. Antonie van Leeuwenhoek 2015; 108:1091-7. [PMID: 26427858 DOI: 10.1007/s10482-015-0562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/19/2015] [Indexed: 11/26/2022]
Abstract
Strain THG-SQA7(T), a Gram-negative, strictly aerobic, non-motile, rod-shaped bacterium was isolated from rhizosphere soil of a rose in PR China. Strain THG-SQA7(T) is closely related to the members of the genus Sphingobium, showing the highest 16S rRNA gene sequence similarities with Sphingobium lactosutens KACC 18100(T) (98.2%) and Sphingobium abikonense KCTC 2864(T) (98.1%). The DNA-DNA relatedness between strain THG-SQA7(T) and S. lactosutens KACC 18100(T) and S. abikonense KCTC 2864(T) was 26.2 ± 0.9 and 28.3 ± 1.2%, respectively. Chemotaxonomic data showed that strain THG-SQA7(T) possesses ubiquinone Q-10 as the predominant respiratory quinone, and C(18:1)ω7c, C(16:0), summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c) and C(14:0) 2OH as the major fatty acids. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, sphingoglycolipid, diphosphatidylglycerol and phosphatidyldimethylethanolamine. Based on these results, together with phenotypic characterization, a novel species, Sphingobium soli sp. nov. is proposed.with the type strain is THG-SQA7(T) (=CCTCC AB 2015125(T) = KCTC 42607(T)).
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Affiliation(s)
- Juan Du
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Hina Singh
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Jung-Eun Yang
- Graduate School of Biotechnology, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Chang Shik Yin
- Department of Acupuncture Meridian Science Research Center, College of Korean Medicine, Kyung Hee University Global Campus, Yongin-si, Republic of Korea
| | - MooChang Kook
- Department of Marine Biotechnology, Anyang University, Incheon, 417-833, Republic of Korea
| | - Hongshan Yu
- College of Bio and Food Technology, Dalian Polytechnic University, Qinggong-yuan No. 1, Ganjingzi-qu, Dalian, 116034, People's Republic of China
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.
- Graduate School of Biotechnology, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea.
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16
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Cai S, Shi C, Zhao JD, Cao Q, He J, Chen LW. Sphingobium phenoxybenzoativorans sp. nov., a 2-phenoxybenzoic-acid-degrading bacterium. Int J Syst Evol Microbiol 2015; 65:1986-1991. [PMID: 25807977 DOI: 10.1099/ijs.0.000209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped bacterium, designated strain SC_3T, was isolated from pesticide-contaminated soil sediment. The strain was able to mineralize 2-phenoxybenzoic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SC_3T formed a monophyletic lineage in the genus Sphingobium, and showed highest similarity to the type strains of Sphingobium abikonense (97.0 %), followed by Sphingobium lactosutens (96.8 %) and Sphingobium cloacae (96.7 %). The DNA-DNA relatedness between strain SC_3T and its closest phylogenetic neighbours was lower than 70 %. The major fatty acids (>5 % of the total) were summed feature 8 (comprising C18:1ω7c/C18:1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c), C14:0 2-OH, C16:0 and C17:1ω6c. The predominant quinone was ubiquinone Q-10, and the major polyamine was spermidine. The polar lipid profile contained diphosphatidylglycerol (DPG), sphingoglycolipid (SGL), phosphatidylethanolamine (PDME), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), an unknown aminolipid (AL), two unknown lipids (L1, L2) and several unknown phospholipids (PL1-6). The genomic DNA G+C content of strain SC_3T was 62.9 mol%. On the basis of phenotypic, chemotaxonomic, phylogenetic and genotypic data, strain SC_3T represents a novel species of the genus Sphingobium, for which the name Sphingobium phenoxybenzoativorans sp. nov. is proposed. The type strain is SC_3T ( = CCTCC AB 2014349T = KACC 42448T).
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Affiliation(s)
- Shu Cai
- College of Life Science, Nanjing Agricultural University, Nanjing, PR China
| | - Chao Shi
- College of Life Science, Nanjing Agricultural University, Nanjing, PR China
| | - Jia-Dong Zhao
- College of Life Science, Nanjing Agricultural University, Nanjing, PR China
| | - Qin Cao
- China National Center for Biotechnology Development, Building 4, No. 16, Xisihuanzhonglu, Haidian District, 100039, Beijing, 100039, PR China
| | - Jian He
- College of Life Science, Nanjing Agricultural University, Nanjing, PR China
| | - Li-Wei Chen
- The College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
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17
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Isolation and the interaction between a mineral-weathering Rhizobium tropici Q34 and silicate minerals. World J Microbiol Biotechnol 2015; 31:747-53. [DOI: 10.1007/s11274-015-1827-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 02/17/2015] [Indexed: 01/09/2023]
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18
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Chen W, Sheng XF, He LY, Huang Z. Rhizobium yantingense sp. nov., a mineral-weathering bacterium. Int J Syst Evol Microbiol 2014; 65:412-417. [PMID: 25376852 DOI: 10.1099/ijs.0.064428-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66(T) and other recognized species of the genus Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)).
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Affiliation(s)
- Wei Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xia-Fang Sheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lin-Yan He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhi Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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19
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Isolation and characterization of fenobucarb-degrading bacteria from rice paddy soils. Biodegradation 2013; 25:383-94. [PMID: 24197220 DOI: 10.1007/s10532-013-9667-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/04/2013] [Indexed: 10/26/2022]
Abstract
Forty-five fenobucarb-degrading bacteria were isolated from rice paddy soils, and their genetic and phenotypic characteristics were investigated. The isolates were able to utilize fenobucarb as a sole source of carbon and energy. Analysis of the 16S rRNA gene sequence indicated that all the isolates were related to members of the genera Sphingobium and Novosphingobium. Among 45 isolates, 21 different chromosomal DNA fingerprinting patterns were obtained. All these strains exhibited similar growth and degradation patterns on fenobucarb. 2-sec-butylphenol was identified as an intermediate during fenobucarb degradation by HPLC analysis. All of the isolates were able to degrade another carbamate insecticide, carbaryl, and 2-sec-butylphenol, but not other fenobucarb related compounds such as aldicarb and fenoxycarb. Representative strains of the different repetitive extragenic palindromic sequence PCR fingerprint types had one to six plasmids. The plasmid-cured strains lost their degradation abilities, suggesting that fenobucarb degradative genes were on their plasmid DNAs in these strains. When analyzed with PCR amplification using the primers targeting for the previously reported carbamate hydrolase genes, most of the isolates did not exhibit any positive signals for different genes involved in carbamate degradation such as mcd, cahA and cehA genes. This is the first report that microorganisms involved in the degradation of fenobucarb have been isolated and the intermediate of fenobucarb biodegradation was identified.
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20
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Li L, Liu H, Shi Z, Wang G. Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus
Sphingobium. Int J Syst Evol Microbiol 2013; 63:604-609. [DOI: 10.1099/ijs.0.040865-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, copper-resistant bacterium, designated strain CU4T, was isolated from copper mine soil in Daye, China. Phylogenetic analysis based on 16S rRNA gene sequences showed highest similarity to
Sphingobium rhizovicinum
CC-FH12-1T (98.4 %), followed by
Sphingobium francense
Sp+T (97.2 %),
Sphingobium japonicum
UT26T (97.1 %),
Sphingobium abikonense
NBRC 16140T (97.0 %),
Sphingobium xenophagum
DSM 6383T (96.9 %) and
Sphingobium yanoikuyae
DSM 7462T (95.5 %). The major fatty acids (>5 %) were summed feature 7 (C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), summed feature 4 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH, and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylcholine. The genomic DNA G+C content of strain CU4T was 64.9 mol%. Comparison of DNA–DNA hybridization, phenotypic and chemotaxonomic characteristics between strain CU4T and phylogenetically related strains revealed that the new isolate represents a novel species of the genus
Sphingobium
, for which the name Sphingobium cupriresistens sp. nov. is proposed. The type strain is CU4T ( = KCTC 23865T = CCTCC AB 2011146T). An emended description of the genus
Sphingobium
is also proposed.
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Affiliation(s)
- Liqiong Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Hongliang Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zunji Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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21
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Tang YQ, Li Y, Zhao JY, Chi CQ, Huang LX, Dong HP, Wu XL. Microbial communities in long-term, water-flooded petroleum reservoirs with different in situ temperatures in the Huabei Oilfield, China. PLoS One 2012; 7:e33535. [PMID: 22432032 PMCID: PMC3303836 DOI: 10.1371/journal.pone.0033535] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 02/10/2012] [Indexed: 11/19/2022] Open
Abstract
The distribution of microbial communities in the Menggulin (MGL) and Ba19 blocks in the Huabei Oilfield, China, were studied based on 16S rRNA gene analysis. The dominant microbes showed obvious block-specific characteristics, and the two blocks had substantially different bacterial and archaeal communities. In the moderate-temperature MGL block, the bacteria were mainly Epsilonproteobacteria and Alphaproteobacteria, and the archaea were methanogens belonging to Methanolinea, Methanothermobacter, Methanosaeta, and Methanocella. However, in the high-temperature Ba19 block, the predominant bacteria were Gammaproteobacteria, and the predominant archaea were Methanothermobacter and Methanosaeta. In spite of shared taxa in the blocks, differences among wells in the same block were obvious, especially for bacterial communities in the MGL block. Compared to the bacterial communities, the archaeal communities were much more conserved within blocks and were not affected by the variation in the bacterial communities.
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Affiliation(s)
- Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yan Li
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Jie-Yu Zhao
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Chang-Qiao Chi
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
| | - Li-Xin Huang
- Research Institute of Petroleum Exploration and Development (Langfang), China National Petroleum Corporation (CNPC), Beijing, People's Republic of China
| | - Han-Ping Dong
- Research Institute of Petroleum Exploration and Development (Langfang), China National Petroleum Corporation (CNPC), Beijing, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, People's Republic of China
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Zhang X, Li B, Wang H, Sui X, Ma X, Hong Q, Jiang R. Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2011; 62:1871-1876. [PMID: 21984664 DOI: 10.1099/ijs.0.026880-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, aerobic, rod-shaped bacteria, designated strains SL-1(T) and F11, which had the ability to decompose polycyclic aromatic hydrocarbons (PAHs), were isolated from soil samples contaminated by oil. The cells were motile by polar or lateral flagella. According to comparison of 16S rRNA gene sequences, strains SL-1(T) and F11 were identical and showed the greatest degree of similarity (96.8%) to both Rhizobium oryzae Alt505(T) and Rhizobium mesosinicum CCBAU 25010(T); however, only Rhizobium oryzae with SL-1(T) and F11 formed a separate clade. There were low similarities (<90%) between the atpD and recA sequences of the two strains and those of the genus of Rhizobium. The bacteria grew at temperatures of 10-40 °C with an optimum of 30 °C. The pH range for growth was 6.0-10.0 and optimum pH was 7.0-8.0. Growth occurred at NaCl concentrations up to 3.0% (w/v). They were catalase- and oxidase-positive. The main cellular fatty acids were summed feature 8 (18:1ω7c and/or 18:1ω6c) and 16:0. The DNA G+C content was 62.2 mol%. Strain SL-1(T) showed 29 and 0% DNA-DNA relatedness, respectively, with the most related strains R. oryzae Alt505(T) and R. mesosinicum CCBAU 25010(T) according to phylogenic analysis of the 16S rRNA gene. According to physiological and biochemical characteristics and genotypic data obtained in this work, the bacteria represent a novel species of the genus Rhizobium, and the name Rhizobium petrolearium is proposed. The type strain is SL-1(T) ( = ACCC 11238(T) = KCTC 23288(T)) and it could nodulate Medicago sativa in nodulation tests.
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Affiliation(s)
- Xiaoxia Zhang
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Baoming Li
- Beijing Centre for Physical and Chemical Analysis, Beijing 100089, PR China
| | - Haisheng Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xinhua Sui
- Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100094, PR China
| | - Xiaotong Ma
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qing Hong
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ruibo Jiang
- Agricultural Culture Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Zhang J, Lang ZF, Zheng JW, Hang BJ, Duan XQ, He J, Li SP. Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system. Int J Syst Evol Microbiol 2011; 62:800-805. [PMID: 21571933 DOI: 10.1099/ijs.0.029827-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-sporulating, non-motile, catalase- and oxidase-positive, Gram-negative, rod-shaped bacterial strain, designated BA-3T, was isolated from activated sludge of a wastewater treatment facility. The strain was able to degrade about 95 % of 100 mg 3-phenoxybenzoic acid l(-1) within 2 days of incubation. Growth occurred in the presence of 0-2 % (w/v) NaCl [optimum, 0.5 % (w/v) NaCl], at pH 5.5-9.0 (optimum, pH 7.0) and at 10-37 °C (optimum, 28 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BA-3T was a member of the genus Sphingobium; it showed highest gene sequence similarity to Sphingobium qiguonii X23T (98.2 %), and similarities of <97.0 % with strains of other Sphingobium species. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of summed feature 8 (C18:1ω6c and/or C18:1ω7c) in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium. Strain BA-3T showed low DNA-DNA relatedness values (21.3±0.8 %) with Sphingobium qiguonii X23(T). Based on phenotypic, genotypic and phylogenetic data, strain BA-3T represents a novel species of the genus Sphingobium, for which the name Sphingobium jiangsuense sp. nov. is proposed; the type strain is BA-3T (=CCTCC AB 2010217T= KCTC 23196T=KACC 16433T).
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Affiliation(s)
- Jun Zhang
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhi-Fei Lang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jin-Wei Zheng
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
| | - Bao-Jian Hang
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiao-Qin Duan
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jian He
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shun-Peng Li
- Key Laboratory for Microbiological Engineering of Agricultural Environment of Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing 210095, PR China
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