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Hu B, Gao S, Zhang H, Li Q, Li G, Zhang S, Xing Y, Huang Y, Han S, Tian Y, Zhang W, He H. Whole-genome sequencing and pathogenicity analysis of Rhodococcus equi isolated in horses. BMC Vet Res 2024; 20:362. [PMID: 39129003 PMCID: PMC11318318 DOI: 10.1186/s12917-024-04167-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/01/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND Rhodococcus equi (R. equi) is a Gram-positive zoonotic pathogen that frequently leads to illness and death in young horses (foals). This study presents the complete genome sequence of R. equi strain BJ13, which was isolated from a thoroughbred racehorse breeding farm in Beijing, China. RESULTS The BJ13 genome has a length of 5.30 Mb and consists of a complete chromosome and a plasmid measuring 5.22 Mb and 0.08 Mb, respectively. We predicted 4,929 coding gene open reading frames, along with 52 tRNAs and 12 rRNAs. Through analysis of mobile genetic elements, we identified 6 gene islands and 1 prophage gene. Pathogenic system analysis predicted the presence of 418 virulence factors and 225 drug resistance genes. Secretion system analysis revealed the prediction of 297 secreted proteins and 1,106 transmembrane proteins. BJ13 exhibits genomic features, virulence-associated genes, potential drug resistance, and a virulence plasmid structure that may contribute to the evolution of its pathogenicity. Lastly, the pathogenicity of the isolated strain was assessed through animal experiments, which resulted in inflammatory reactions or damage in the lungs, liver, and spleen of mice. Moreover, by the 7th day post-infection, the mortality rate of the mice reached 50.0%, indicating complex immune regulatory mechanisms, including overexpression of IL-10 and increased production of pro-inflammatory cytokines like TNF-α. These findings validate the strong pathogenicity of the isolated strain and provide insights for studying the pathogenic mechanisms of Rhodococcus equi infection. CONCLUSIONS The complete genome sequence of R. equi strain BJ13 provides valuable insights into its genomic characteristics, virulence potential, drug resistance, and secretion systems. The strong pathogenicity observed in animal experiments underscores the need for further investigation into the pathogenic mechanisms of R. equi infection.
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Affiliation(s)
- Bin Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sichao Gao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Anhui University of Science and Technology, Huainan, China
| | - Hao Zhang
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoqiao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Anhui University of Science and Technology, Huainan, China
| | - Gaojian Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuairan Zhang
- College of Shenyang Institute of Technology, Shenyang, Liaoning, China
| | - Yanan Xing
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyi Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Tian
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, China
| | - Wei Zhang
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, China
| | - Hongxuan He
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
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Xiao Y, Dong M, Yang B, Wang S, Liang S, Liu D, Zhang H. Strengthening bioremediation potential: Enterobacter ludwigii ES2 for combined nicosulfuron and Cd contamination through whole genome and microbial diversity community analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135476. [PMID: 39137549 DOI: 10.1016/j.jhazmat.2024.135476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/11/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
Nicosulfuron and Cd are common pollutants that pose significant threats to the environment and human health, particularly under combined stress. This study is the first to remediate environmental nicosulfuron and Cd under combined stress using microbiological techniques. Enterobacter ludwigii ES2 was isolated, characterized, and demonstrated to degrade 93.80 % of nicosulfuron and remove 59.64 % of Cd within 4 d. Potential functional genes, including nicosulfuron degradation genes gstA, gstB, glnQ, glnP, mreB, and sixA, and Cd tolerance/removal-related genes mntA, mntB, mntH, dnaK, znuA, and zupt, were predicted by sequencing the whole genome of strain ES2, and their expression was verified by qRT-PCR. Strain ES2 managed oxidative stress induced by Cd through superoxide dismutase, glutathione, catalase, peroxidase, and malondialdehyde. Furthermore, to repair compound stress, up to 90.48 % of nicosulfuron and 67.74 % of Cd were removed. The community structure analysis indicated that Enterobacteriaceae, Sphingomonadaceae, and Gemmatimonadaceae were dominant populations, with ES2 stably colonizing and becoming the dominant bacterium. In summary, ES2 demonstrated significant potential in remediating nicosulfuron and Cd pollution from various perspectives, providing a solid theoretical foundation.
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Affiliation(s)
- Yufeng Xiao
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Meiqi Dong
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Bingbing Yang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Siya Wang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Shuang Liang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
| | - Donghui Liu
- Department of Applied Chemistry, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing 100193, China.
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
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3
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Zhai Q, Zheng S, Zhang C, Lu Z, Liang S, Li R, Zhang X, Pan H, Zhang H. Kj-mhpC Enzyme in Klebsiella jilinsis 2N3 Is Involved in the Degradation of Chlorimuron-Ethyl via De-Esterification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5176-5184. [PMID: 38417018 DOI: 10.1021/acs.jafc.3c08918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Microbial degradation is a highly efficient and reliable approach for mitigating the contamination of sulfonylurea herbicides, such as chlorimuron-ethyl, in soil and water. In this study, we aimed to assess whether Kj-mhpC plays a pivotal role in the degradation of chlorimuron-ethyl. Kj-mhpC enzyme purified via prokaryotic expression exhibited the highest catalytic activity for chlorimuron-ethyl at 35 °C and pH 7. Bioinformatic analysis and three-dimensional homologous modeling of Kj-mhpC were conducted. Additionally, the presence of Mg+ and Cu2+ ions partially inhibited but Pb2+ ions completely inhibited the enzymatic activity of Kj-mhpC. LC/MS revealed that Kj-mhpC hydrolyzes the ester bond of chlorimuron-ethyl, resulting in the formation of 2-(4-chloro-6-methoxypyrimidine-2-amidoformamidesulfonyl) benzoic acid. Furthermore, the point mutation of serine at position 67 (Ser67) confirmed that it is the key amino acid at the active site for degrading chlorimuron-ethyl. This study enhanced the understanding of how chlorimuron-ethyl is degraded by microorganisms and provided a reference for bioremediation of the environment polluted with chlorimuron-ethyl.
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Affiliation(s)
- Qianhang Zhai
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shuanglan Zheng
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zhou Lu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shuang Liang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Ranhong Li
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xianghui Zhang
- College of Plant Science, Jilin University, Changchun 130118, China
| | - Hongyu Pan
- College of Plant Science, Jilin University, Changchun 130118, China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
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4
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Zhu DH, Nie FH, Song QL, Wei W, Zhang M, Hu Y, Lin HY, Kang DJ, Chen ZB, Chen JJ. Isolation and genomic characterization of Klebsiella Lw3 with polychlorinated biphenyl degradability. ENVIRONMENTAL TECHNOLOGY 2023; 44:3656-3666. [PMID: 35441572 DOI: 10.1080/09593330.2022.2068381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as Klebsiella Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography-mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for Klebsiella research with practical significance for in situ bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
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Affiliation(s)
- Di-Hua Zhu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Fang-Hong Nie
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Qing-Lang Song
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Wan Wei
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Min Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Yao Hu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Hong-Ying Lin
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Dan-Ju Kang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Zhi-Bao Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Jin-Jun Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
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5
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Yu Z, Dai Y, Li T, Gu W, Yang Y, Li X, Peng P, Yang L, Li X, Wang J, Su Z, Li X, Xu M, Zhang H. A Novel Pathway of Chlorimuron-Ethyl Biodegradation by Chenggangzhangella methanolivorans Strain CHL1 and Its Molecular Mechanisms. Int J Mol Sci 2022; 23:ijms23179890. [PMID: 36077288 PMCID: PMC9456165 DOI: 10.3390/ijms23179890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/21/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chlorimuron-ethyl is a widely used herbicide in agriculture. However, uncontrolled chlorimuron-ethyl application causes serious environmental problems. Chlorimuron-ethyl can be effectively degraded by microbes, but the underlying molecular mechanisms are not fully understood. In this study, we identified the possible pathways and key genes involved in chlorimuron-ethyl degradation by the Chenggangzhangella methanolivorans strain CHL1, a Methylocystaceae strain with the ability to degrade sulfonylurea herbicides. Using a metabolomics method, eight intermediate degradation products were identified, and three pathways, including a novel pyrimidine-ring-opening pathway, were found to be involved in chlorimuron-ethyl degradation by strain CHL1. Transcriptome sequencing indicated that three genes (atzF, atzD, and cysJ) are involved in chlorimuron-ethyl degradation by strain CHL1. The gene knock-out and complementation techniques allowed for the functions of the three genes to be identified, and the enzymes involved in the different steps of chlorimuron-ethyl degradation pathways were preliminary predicted. The results reveal a previously unreported pathway and the key genes of chlorimuron-ethyl degradation by strain CHL1, which have implications for attempts to enrich the biodegradation mechanism of sulfonylurea herbicides and to construct engineered bacteria in order to remove sulfonylurea herbicide residues from environmental media.
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Affiliation(s)
- Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Basic Medical College, Shenyang Medical College, Shenyang 100034, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang 110021, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Pai Peng
- Shenyang Research Institute of Chemical Industry, Shenyang 110021, China
| | - Lijie Yang
- Shenyang Research Institute of Chemical Industry, Shenyang 110021, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jian Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Correspondence: (M.X.); (H.Z.)
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Correspondence: (M.X.); (H.Z.)
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6
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Yu Z, Gu W, Yang Y, Li X, Li X, Li T, Wang J, Su Z, Li X, Dai Y, Xu M, Zhang H. Whole-Genome Sequencing of a Chlorimuron-Ethyl-Degrading Strain: Chenggangzhangella methanolivorans CHL1 and Its Degrading Enzymes. Microbiol Spectr 2022; 10:e0182222. [PMID: 35861510 PMCID: PMC9430300 DOI: 10.1128/spectrum.01822-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, and its long-term residues cause serious environmental problems. Biodegradation of chlorimuron-ethyl is effective and feasible, and many degrading strains have been obtained, but still, the genes and enzymes involved in this degradation are often unclear. In this study, whole-genome sequencing was performed on chlorimuron-ethyl-degrading strain, Chenggangzhangella methanolivorans CHL1. The complete genome of strain CHL1 contains one circular chromosome of 5,542,510 bp and a G+C content of 68.17 mol%. Three genes, sulE, pnbA, and gst, were predicted to be involved in the degradation of chlorimuron-ethyl, and this was confirmed by gene knockout and gene complementation experiments. The three genes were cloned and expressed in Escherichia coli BL21 (DE3) to allow for the evaluation of the catalytic activities of the respective enzymes. The glutathione-S-transferase (GST) catalyzes the cleavage of the sulfonylurea bridge of chlorimuron-ethyl, and the esterases, PnbA and SulE, both de-esterify it. This study identifies three key functional genes of strain CHL1 that are involved in the degradation of chlorimuron-ethyl and also provides new approaches by which to construct engineered bacteria for the bioremediation of environments polluted with sulfonylurea herbicides. IMPORTANCE Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, worldwide. However, its residues in soil and water have a potent toxicity toward sensitive crops and other organisms, such as microbes and aquatic algae, and this causes serious problems for the environment. Microbial degradation has been demonstrated to be a feasible and promising strategy by which to eliminate xenobiotics from the environment. Many chlorimuron-ethyl-degrading microorganisms have been reported, but few studies have investigated the genes and enzymes that are involved in the degradation. In this work, two esterase-encoding genes (sulE, pnbA) and a glutathione-S-transferase-encoding gene (gst) responsible for the detoxification of chlorimuron-ethyl by strain Chenggangzhangella methanolivorans CHL1 were identified, then cloned and expressed in Escherichia coli BL21 (DE3). These key chlorimuron-ethyl-degrading enzymes are candidates for the construction of engineered bacteria to degrade this pesticide and enrich the resources for bioremediating environments polluted with sulfonylurea herbicides.
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Affiliation(s)
- Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang, China
| | - Jian Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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7
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Tahir U, Yasmin A. Decolorization and discovery of metabolic pathway for the degradation of Mordant Black 11 dye by Klebsiella sp. MB398. Braz J Microbiol 2021; 52:761-771. [PMID: 33754316 DOI: 10.1007/s42770-021-00470-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/16/2021] [Indexed: 10/21/2022] Open
Abstract
Extensive utilization of the synthetic dyes in various industries is leading to water and soil contamination and ultimately impacting the humans. A research study was conducted for investigating the biodecolorization and biotransformation of Mordant Black 11 dye. For this purpose, potential of biofilm forming bacteria Klebsiella pneumoniae MB398 isolated from effluent outlets of Tops Food Industry, Hattar, Pakistan, was assessed to decolorize and transform Mordant Black 11 dye. Bacterial strain MB398 exhibited the capability of growing optimally at acidic pH (pH 6.0). Klebsiella pneumoniae MB398 efficiently decolorized Mordant Black 11 dye (64.55%) in aerobic environment at pH 6.0 and 37 °C over 24 h, which further increased to 75.35% over a period of 72 h of incubation. Strain MB398 also exhibited the capability of decolorizing Mordant Black 11 dye in the presence of cadmium (63.71%), chromium (61.78%), and copper (61.50%), respectively. UV-VIS spectrophotometric analysis, FTIR, and HPLC spectra were also indicative of biotransformation of dye molecules by Klebsiella pneumoniae MB398. GC-MS analysis of Mordant Black 11 dye revealed formation of 9 novel and unique metabolites including phenol,2,4-bis(1,1-dimethylethyl); 9-eicosene, (E); ethanol,2,2-(2-propenyloxy); acetic acid, benzene; 1-naphthol; methyl formate; valeraldehyde,2,4-dimethyl; and 7-hexadecene (Z). A possible metabolic pathway depicting the biotransformation of Mordant Black 11 dye by Klebsiella pneumoniae MB398 was projected. Findings of the current research study strongly suggest application of Klebsiella pneumoniae MB398 for developing large scale bioremediation strategies for the abatement of synthetic dyes to retain environmental sustainability in bioeconomic way.
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Affiliation(s)
- Uruj Tahir
- Department of Environmental Sciences, Microbiology and Biotechnology Laboratory, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan. .,Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan. .,Department of Environmental Sciences, Faculty of Natural Sciences, University of Okara, Okara, 56130, Pakistan.
| | - Azra Yasmin
- Department of Environmental Sciences, Microbiology and Biotechnology Laboratory, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.,Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan
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8
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Oyewusi HA, Wahab RA, Huyop F. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Mol Biol Rep 2021; 48:2687-2701. [PMID: 33650078 DOI: 10.1007/s11033-021-06239-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB 5351, Ado Ekiti, Ekiti State, Nigeria.
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
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9
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Pileggi M, Pileggi SA, Sadowsky MJ. Herbicide bioremediation: from strains to bacterial communities. Heliyon 2020; 6:e05767. [PMID: 33392402 PMCID: PMC7773584 DOI: 10.1016/j.heliyon.2020.e05767] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/23/2020] [Accepted: 12/15/2020] [Indexed: 01/12/2023] Open
Abstract
There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics. With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without causing other environmental impacts not anticipated by simpler approaches. The understanding of microbial community dynamics in free-living microbiota and those present in complex communities and in biofilms is paramount to achieving these objectives. It is also essential that non-developed countries, which are major food producers and consumers of pesticides, have access to these techniques to achieve sustainable production, without causing impacts through unknown side effects.
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Affiliation(s)
- Marcos Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Sônia A.V. Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Michael J. Sadowsky
- The Biotechnology Institute, Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
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Zhang C, Hao Q, Zhang S, Zhang Z, Zhang X, Sun P, Pan H, Zhang H, Sun F. Transcriptomic analysis of Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 183:109581. [PMID: 31446172 DOI: 10.1016/j.ecoenv.2019.109581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Chlorimuron-ethyl is a sulfonylurea herbicide with a long residual period in the field and is toxic to rotational crops. Klebsiella jilinsis 2N3 is a gram-negative bacterium that can rapidly degrade Chlorimuron-ethyl. In this study, the gene expression changes in strain 2N3 during degradation of Chlorimuron-ethyl was analyzed by RNA-Seq. Results showed that 386 genes were up-regulated and 453 genes were down-regulated. KEGG pathway enrichment analysis revealed the highest enrichment ratio in the pathway of sulfur metabolism. On the basis of the functional annotation and gene expression, we predicted that carboxylesterase, monooxygenase, glycosyltransferase, and cytochrome P450 were involved in the metabolism of Chlorimuron-ethyl biodegradation. Results of qRT-PCR showed that the relative mRNA expression levels of these genes were higher in treatment group than those in control group. The cytochrome P450 encoded by Kj-CysJ and the alkanesulfonate monooxygenase encoded by Kj-SsuD were predicted and further experimentally confirmed by gene knockout as the key enzymes in the biodegradation process. Cultured in basal medium containing Chlorimuron-ethyl (5 mg L-1) in 36 h, the strains of ΔKj-CysJ, ΔKj-SsuD, and WT reached the highest OD600 values of 0.308, 0.873, and 1.085, and the highest degradation rates of Chlorimuron-ethyl of 11.83%, 96.21%, and 95.62%, respectively.
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Affiliation(s)
- Cheng Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Qingkai Hao
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Sisheng Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Zhengyi Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Peng Sun
- Department of Computer Science, Iowa State University, Ames, IA, USA, 50011
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Hao Zhang
- College of Resource and Environment, Jilin Agricultural University, Changchun, 130118, PR China.
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USA, 30024.
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