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Li Q, Ma Q, Zhou Y, Jiang X, Parales RE, Zhao S, Zhuang Y, Ruan Z. Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134951. [PMID: 38917628 DOI: 10.1016/j.jhazmat.2024.134951] [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: 03/20/2024] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024]
Abstract
Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L-1 mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.
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Affiliation(s)
- Qingqing Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyun Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Zhou
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Jiang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Shumiao Zhao
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhuang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyong Ruan
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Li Y, Qiu J, Yang J, Li Y, Zhang H, Zhao F, Tan H. Molecular Mechanism of GmSNE3 Ubiquitin Ligase-Mediated Inhibition of Soybean Nodulation by Halosulfuron Methyl. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14114-14125. [PMID: 38867659 DOI: 10.1021/acs.jafc.4c02621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In this study, the role of E3 ubiquitin ligase GmSNE3 in halosulfuron methyl (HSM) inhibiting soybean nodulation was investigated. GmSNE3 was strongly induced by HSM stress, and the overexpression of GmSNE3 significantly reduced the number of soybean nodules. Further investigation found that GmSNE3 could interact with a nodulation signaling pathway 1 protein (GmNSP1a) and GmSNE3 could mediate the degradation of GmNSP1a. Importantly, GmSNE3-mediated degradation of GmNSP1a could be promoted by HSM stress. Moreover, HSM stress and the overexpression of GmSNE3 resulted in a substantial decrease in the expression of the downstream target genes of GmNSP1a. These results revealed that HSM promotes the ubiquitin-mediated degradation of GmNSP1a by inducing GmSNE3, thereby inhibiting the regulatory effect of GmNSP1a on its downstream target genes and ultimately leading to a reduction in nodulation. Our findings will promote a better understanding of the toxic mechanism of herbicides on the symbiotic nodulation between legumes and rhizobia.
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Affiliation(s)
- Yuanfu Li
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Jingsi Qiu
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Jingxia Yang
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Yihan Li
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Hui Zhang
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Feng Zhao
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Huihua Tan
- Guangxi Key Laboratory for Agro-Environment and Agric-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
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Lei Q, Zhong J, Chen SF, Wu S, Huang Y, Guo P, Mishra S, Bhatt K, Chen S. Microbial degradation as a powerful weapon in the removal of sulfonylurea herbicides. ENVIRONMENTAL RESEARCH 2023; 235:116570. [PMID: 37423356 DOI: 10.1016/j.envres.2023.116570] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/25/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023]
Abstract
Sulfonylurea herbicides have been widely used worldwide and play a significant role in modern agricultural production. However, these herbicides have adverse biological effects that can damage the ecosystems and harm human health. As such, rapid and effective techniques that remove sulfonylurea residues from the environment are urgently required. Attempts have been made to remove sulfonylurea residues from environment using various techniques such as incineration, adsorption, photolysis, ozonation, and microbial degradation. Among them, biodegradation is regarded as a practical and environmentally responsible way to eliminate pesticide residues. Microbial strains such as Talaromyces flavus LZM1, Methylopila sp. SD-1, Ochrobactrum sp. ZWS16, Staphylococcus cohnii ZWS13, Enterobacter ludwigii sp. CE-1, Phlebia sp. 606, and Bacillus subtilis LXL-7 can almost completely degrade sulfonylureas. The degradation mechanism of the strains is such that sulfonylureas can be catalyzed by bridge hydrolysis to produce sulfonamides and heterocyclic compounds, which deactivate sulfonylureas. The molecular mechanisms associated with microbial degradation of sulfonylureas are relatively poorly studied, with hydrolase, oxidase, dehydrogenase and esterase currently known to play a pivotal role in the catabolic pathways of sulfonylureas. Till date, there are no reports specifically on the microbial degrading species and biochemical mechanisms of sulfonylureas. Hence, in this article, the degradation strains, metabolic pathways, and biochemical mechanisms of sulfonylurea biodegradation, along with its toxic effects on aquatic and terrestrial animals, are discussed in depth in order to provide new ideas for remediation of soil and sediments polluted by sulfonylurea herbicides.
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Affiliation(s)
- Qiqi Lei
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Jianfeng Zhong
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Shao-Fang Chen
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Siyi Wu
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yaohua Huang
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Peng Guo
- Zhongshan City Garden Management Center of Guangdong Province, Zhongshan, China
| | - Sandhya Mishra
- Environmental Technologies Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, USA.
| | - Shaohua Chen
- National Key Laboratory of Green Pesticide, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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Wu T, Guo SZ, Zhu HZ, Yan L, Liu ZP, Li DF, Jiang CY, Corvini PFX, Shen XH, Liu SJ. The sulfonamide-resistance dihydropteroate synthase gene is crucial for efficient biodegradation of sulfamethoxazole by Paenarthrobacter species. Appl Microbiol Biotechnol 2023; 107:5813-5827. [PMID: 37439835 DOI: 10.1007/s00253-023-12679-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023]
Abstract
Sulfonamide antibiotics (SAs) are serious pollutants to ecosystems and environments. Previous studies showed that microbial degradation of SAs such as sulfamethoxazole (SMX) proceeds via a sad-encoded oxidative pathway, while the sulfonamide-resistant dihydropteroate synthase gene, sul, is responsible for SA resistance. However, the co-occurrence of sad and sul genes, as well as how the sul gene affects SMX degradation, was not explored. In this study, two SMX-degrading bacterial strains, SD-1 and SD-2, were cultivated from an SMX-degrading enrichment. Both strains were Paenarthrobacter species and were phylogenetically identical; however, they showed different SMX degradation activities. Specifically, strain SD-1 utilized SMX as the sole carbon and energy source for growth and was a highly efficient SMX degrader, while SD-2 did could not use SMX as a sole carbon or energy source and showed limited SMX degradation when an additional carbon source was supplied. Genome annotation, growth, enzymatic activity tests, and metabolite detection revealed that strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation and a pathway of protocatechuate degradation. A new sulfonamide-resistant dihydropteroate synthase gene, sul918, was identified in strain SD-1, but not in SD-2. Moreover, the lack of sul918 resulted in low SMX degradation activity in strain SD-2. Genome data mining revealed the co-occurrence of sad and sul genes in efficient SMX-degrading Paenarthrobacter strains. We propose that the co-occurrence of sulfonamide-resistant dihydropteroate synthase and sad genes is crucial for efficient SMX biodegradation. KEY POINTS: • Two sulfamethoxazole-degrading strains with distinct degrading activity, Paenarthrobacter sp. SD-1 and Paenarthrobacter sp. SD-2, were isolated and identified. • Strains SD-1 and SD-2 shared a sad-encoded oxidative pathway for SMX degradation. • A new plasmid-borne SMX resistance gene (sul918) of strain SD-1 plays a crucial role in SMX degradation efficiency.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sheng-Zhi Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Yan
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xi-Hui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Zhong J, Wu S, Chen WJ, Huang Y, Lei Q, Mishra S, Bhatt P, Chen S. Current insights into the microbial degradation of nicosulfuron: Strains, metabolic pathways, and molecular mechanisms. CHEMOSPHERE 2023; 326:138390. [PMID: 36935058 DOI: 10.1016/j.chemosphere.2023.138390] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/02/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Nicosulfuron is among the sulfonylurea herbicides that are widely used to control annual and perennial grass weeds in cornfields. However, nicosulfuron residues in the environment are likely to cause long-lasting harmful environmental and biological effects. Nicosulfuron degrades via photo-degradation, chemical hydrolysis, and microbial degradation. The latter is crucial for pesticide degradation and has become an essential strategy to remove nicosulfuron residues from the environment. Most previous studies have focused on the screening, degradation characteristics, and degradation pathways of biodegrader microorganisms. The isolated nicosulfuron-degrading strains include Bacillus, Pseudomonas, Klebsiella, Alcaligenes, Rhodopseudomonas, Ochrobactrum, Micrococcus, Serratia, Penicillium, Aspergillus, among others, all of which have good degradation efficiency. Two main intermediates, 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), are produced during microbial degradation and are derived from the C-N, C-S, and S-N bond breaks on the sulfonylurea bridge, covering almost every bacterial degradation pathway. In addition, enzymes related to the degradation of nicosulfuron have been identified successively, including the manganese ABC transporter (hydrolase), Flavin-containing monooxygenase (oxidase), and E3 (esterase). Further in-depth studies based on molecular biology and genetics are needed to elaborate on their role in the evolution of novel catabolic pathways and the microbial degradation of nicosulfuron. To date, few reviews have focused on the microbial degradation and degradation mechanisms of nicosulfuron. This review summarizes recent advances in nicosulfuron degradation and comprehensively discusses the potential of nicosulfuron-degrading microorganisms for bioremediating contaminated environments, providing a reference for further research development on nicosulfuron biodegradation in the future.
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Affiliation(s)
- Jianfeng Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Siyi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Sandhya Mishra
- Environmental Technologies Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, 47906, USA.
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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6
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Hassan S, Ganai BA. Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review. World J Microbiol Biotechnol 2023; 39:151. [PMID: 37029313 DOI: 10.1007/s11274-023-03603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Vanitha TK, Suresh G, Bhandi MM, Mudiam MKR, Mohan SV. Microbial degradation of organochlorine pesticide: 2,4-Dichlorophenoxyacetic acid by axenic and mixed consortium. BIORESOURCE TECHNOLOGY 2023; 382:129031. [PMID: 37037331 DOI: 10.1016/j.biortech.2023.129031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 05/31/2023]
Abstract
The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.
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Affiliation(s)
- T K Vanitha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - G Suresh
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India
| | - Murali Mohan Bhandi
- Analytical & Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohana Krishna Reddy Mudiam
- Analytical & Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, Telangana 500 007, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Ma Q, Han X, Song J, Wang J, Li Q, Parales RE, Li L, Ruan Z. Characterization of a new chlorimuron-ethyl-degrading strain Cedecea sp. LAM2020 and biodegradation pathway revealed by multiomics analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130197. [PMID: 36272371 DOI: 10.1016/j.jhazmat.2022.130197] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/24/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The widespread use of the herbicide chlorimuron-methyl is hazard to rotational crops and causes soil degradation problems. Biodegradation is considered a promising way for removing herbicide residues from the environment. Here, a new isolated strain, Cedecea sp. LAM2020, enabled complete degradation of 100 mg/L chlorimuron-methyl within five days. Transcriptome analysis revealed that ABC transporters, atrazine degradation and purine metabolism were enriched in the KEGG pathway. Integrating GO and KEGG classification with related reports, we predict that carboxylesterases are involved in the biodegradation of chlorimuron-methyl by LAM2020. Heterologous expression of the carboxylesterase gene carH showed 26.67% degradation of 50 mg/L chlorimuron-methyl within 6 h. The intracellular potential biological response and extracellular degradation process of chlorimuron-ethyl were analyzed by the nontarget metabolomic and mass spectrometry respectively, and the biodegradation characteristics and complete mineralization pathway was revealed. The cleavage of the sulfonylurea bridge and the ester bond achieved the first step in the degradation of chlorimuron-methyl. Together, these results reveal the presence of acidolysis and enzymatic degradation of chlorimuron-methyl by strain LAM2020. Hydroponic corn experiment showed that the addition of strain LAM2020 alleviated the toxic effects of chlorimuron-ethyl on the plants. Collectively, strain LAM2020 may be a promising microbial agent for plants chlorimuron-ethyl detoxification and soil biofertilizer.
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Affiliation(s)
- Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiaoyan Han
- Autobio Diagnostics Co., Ltd., 450016, China
| | - Jinlong Song
- Chinese Academy of Fishery Sciences, Beijing 100081, PR China
| | - Jie Wang
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, PR China; College of Life Sciences, Yantai University, Yantai 264005, PR China.
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9
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Yang D, Huo J, Zhang Z, An Z, Dong H, Wang Y, Duan W, Chen L, He M, Gao S, Zhang J. Citric acid modified ultrasmall copper peroxide nanozyme for in situ remediation of environmental sulfonylurea herbicide contamination. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130265. [PMID: 36327847 DOI: 10.1016/j.jhazmat.2022.130265] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Herbicide residues in the environment threaten high-quality agriculture and human health. Consequently, in situ remediation of herbicide contamination is vital. We synthesized a novel self-catalyzed nanozyme, ultrasmall (2-3 nm) copper peroxide nanodots modified by citric acid (CP@CA) for this purpose, which can break down into H2O2 and Cu2+ in water or soil. Ubiquitous glutathione reduces Cu2+ into Cu+, which promotes the decomposition of H2O2 into •OH through a Fenton-like reaction under mild acid conditions created by the presence of citric acid. The generated •OH efficiently degrade nicosulfuron in water and soil, and the maximum degradation efficiency could be achieved at 97.58% in water at 56 min. The possible degradation mechanisms of nicosulfuron were proposed through the 25 intermediates detected. The overall ecotoxicity of the nicosulfuron system was significantly reduced after CP@CA treatment. Furthermore, CP@CA had little impact on active components of soil bacterial community. Moreover, CP@CA nanozyme could effectively remove seven other sulfonylurea herbicides from the water. In this paper, a high-efficiency method for herbicide degradation was proposed, which provides a new reference for the in situ remediation of herbicide pollution.
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Affiliation(s)
- Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jingqian Huo
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Zhe Zhang
- School of Engineering, Westlake University, Hangzhou 310024, China
| | - Zexiu An
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China; Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Haijiao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding 071000, China
| | - Yanen Wang
- College of Science, Hebei Agricultural University, Baoding 071001, China
| | - Weidi Duan
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Lai Chen
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Maoxia He
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Shutao Gao
- College of Science, Hebei Agricultural University, Baoding 071001, China.
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China.
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10
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Li Q, Wang J, Ma Q, Han X, Zhang W, Ruan Z. Cedecea sulfonylureivorans sp. nov., a novel chlorimuron-ethyldegrading bacterium isolated from an herbicides-degrading consortium. Arch Microbiol 2022; 205:21. [PMID: 36484840 DOI: 10.1007/s00203-022-03362-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
A Gram-stain-negative, motile, rod-shaped bacterium, designated strain LAM2020T, was isolated from a sulfonylurea herbicides-degrading bacterial consortium. The optimal temperature and pH for the growth of strain LAM2020T were 30 °C and 7.0, respectively. Strain LAM2020T formed a distinct phylogenetic subclade within the genus Cedecea in the phylogenetic trees built with 16S rRNA gene sequences and shared the highest similarity with Cedecea davisae DSM 4568T (98.4%). The values of digital DNA-DNA hybridization and average nucleotide identity (ANI) based on the genome sequences between LAM2020T and C. davisae DSM 4568T were 22.7% and 80.0%, respectively. It contained 54.0 mol% of G + C in the genomic DNA. The major cellular fatty acids of strain LAM2020T were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0 and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The major polar lipids present in strain LAM2020T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The respiratory quinone of strain LAM2020T was ubiquinone-8 and ubiquinone-7. Based on the phenotypic characteristics, chemotaxonomic data and genotypic analyses, strain LAM2020T should be classified as a novel species of genus Cedecea, for which the name Cedecea sulfonylureivorans sp. nov. is proposed. The type strain is LAM2020T (= GDMCC 1.2363T = JCM 34640T).
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Affiliation(s)
- Qingqing Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Wang
- College of Life Science, Xinjiang Normal University, Urumqi, 830054, China
| | - Qingyun Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoyan Han
- Autobio Diagnostics Co., Ltd., Zhengzhou, 450016, China
| | - Wei Zhang
- College of Life Science, Xinjiang Normal University, Urumqi, 830054, China.
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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11
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A water-stable Eu-MOF as multi-responsive luminescent sensor for high-efficiency detection of Fe3+, MnO4− ions and nicosulfuron in aqueous solution. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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12
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Li Y, Yu H, Liu L, Liu Y, Huang L, Tan H. Transcriptomic and physiological analyses unravel the effect and mechanism of halosulfuron-methyl on the symbiosis between rhizobium and soybean. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114248. [PMID: 36332406 DOI: 10.1016/j.ecoenv.2022.114248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Halosulfuron-methyl (HSM) is a new and highly effective sulfonylurea herbicide widely used in weed control, but its residue in the environment poses a potential risk to soybean. Soybean-rhizobium symbiotic nitrogen fixation is crucial for sustainable agricultural development and ecological environment health. However, the impact of HSM on the symbiosis between soybean and rhizobium is unclear. In this study, the effects of HSM on the soybean-rhizobium symbiotic process and nitrogen fixation were investigated by means of transcriptomic and physiological analyses. Treatment with a concentration of HSM less than 0.5 mg L-1 had no effect on rhizobium growth, but significantly reduced nodules number, the biomass of soybean nodules, and nitrogenase activity in root nodules (P < 0.05). Transcriptomic analysis showed that differentially expressed genes (DEGs) involved in NH4+ assimilation were significantly downregulated (P < 0.05). In addition, the activities of NH4+ assimilation enzymes were markedly reduced. This result was further confirmed by the accumulation of NH4+ in root nodules, indicating that the inhibition of nitrogen fixation by HSM may be caused by excessive NH4+ accumulation in root nodules. Furthermore, DEGs involved in flavonoid synthesis, phytohormone biosynthesis, and phytohormone signaling transduction were significantly downregulated (P < 0.05), which was consistent with the decrease in flavonoid and phytohormone contents determined in this study. These results suggested that HSM may inhibit soybean nodulation by inhibiting flavonoid synthesis in soybean roots, disrupting the balance of plant endogenous hormones in roots during symbiosis, and blocking the transmission of hormone signals during the symbiosis. Our findings provide new insights into the effects of HSM on the legume-rhizobium nodule symbiotic process.
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Affiliation(s)
- Yuanfu Li
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Huan Yu
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Li Liu
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yanmei Liu
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Lulu Huang
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Huihua Tan
- Guangxi Key Laboratory for Agro-Environment and Agro, Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China.
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13
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Ma Q, Tan H, Song J, Li M, Wang Z, Parales RE, Li L, Ruan Z. Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119477. [PMID: 35598816 DOI: 10.1016/j.envpol.2022.119477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.
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Affiliation(s)
- Qingyun Ma
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Hao Tan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jinlong Song
- Chinese Academy of Fishery Sciences, Beijing, 100141, PR China
| | - Miaomiao Li
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, PR China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Zhiyong Ruan
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi, 860000, PR China; College of Life Sciences, Yantai University, Yantai, 264005, PR China.
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14
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Transcriptomic response of Pseudomonas nicosulfuronedens LAM1902 to the sulfonylurea herbicide nicosulfuron. Sci Rep 2022; 12:13656. [PMID: 35953636 PMCID: PMC9372043 DOI: 10.1038/s41598-022-17982-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/03/2022] [Indexed: 12/13/2022] Open
Abstract
The overuse of the herbicide nicosulfuron has become a global environmental concern. As a potential bioremediation technology, the microbial degradation of nicosulfuron shows much promise; however, the mechanism by which microorganisms respond to nicosulfuron exposure requires further study. An isolated soil-borne bacteria Pseudomonas nicosulfuronedens LAM1902 displaying nicosulfuron, chlorimuron-ethyl, and cinosulfuron degradabilities in the presence of glucose, was used to determine the transcriptional responses to nicosulfuron exposure. RNA-Seq results indicated that 1102 differentially expressed genes (DEGs) were up-regulated and 702 down-regulated under nicosulfuron stress. DEGs were significantly enriched in “ABC transporters”, “sulfur metabolism”, and “ribosome” pathways (p ≤ 0.05). Several pathways (glycolysis and pentose phosphate pathways, a two-component regulation system, as well as in bacterial chemotaxis metabolisms) were affected by nicosulfuron exposure. Surprisingly, nicosulfuron exposure showed positive effects on the production of oxalic acid that is synthesized by genes encoding glycolate oxidase through the glyoxylate cycle pathway. The results suggest that P. nicosulfuronedens LAM1902 adopt acid metabolites production strategies in response to nicosulfuron, with concomitant nicosulfuron degradation. Data indicates that glucose metabolism is required during the degradation and adaptation of strain LAM1902 to nicosulfuron stress. The present studies provide a glimpse at the molecular response of microorganisms to sulfonylurea pesticide toxicity and a potential framework for future mechanistic studies.
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15
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Zhao C, He X, Dan X, He M, Zhao J, Meng H, Cai Z, Zhang J. Soil dissolved organic matters mediate bacterial taxa to enhance nitrification rates under wheat cultivation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154418. [PMID: 35276137 DOI: 10.1016/j.scitotenv.2022.154418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Studies have shown that dissolved organic matters (DOMs) may affect soil nutrient availability to plants due to their effect on microbial communities; however, the relationships of soil DOM-bacterial community-N function in response to root exudates remains poorly understand. Here, we evaluated the DOM composition, bacterial taxonomic variation and nitrogen transformation rates in both acidic and alkaline soils, with or without the typical nitrate preference plant (wheat, Triticum aestivum L.). After 30 days' cultivation, DOM compositions such as sugars, amines, amino acids, organic acid, and ketone were significantly increased in soil with wheat vs. bare soil, and these compounds were mainly involved in nitrogen metabolism pathways. Soil core bacterial abundance was changed while bacterial community diversity decreased in response to wheat planting. Function prediction analysis based on FAPROTAX software showed that the bacterial community were significantly (p < 0.05) affiliated with nitrification and organic compound degradation. Additionally, db-RDA and VPA analysis suggested that the contribution of soil DOM to the variance of bacterial community was stronger than that of soil available nutrients. Furthermore, the N-transformation related bacteria like Burkholderiales and ammonia-oxidizing bacteria (AOB) were positively correlated with soil gross nitrification rate, confirming that the soil N transformation was enhanced in both acidic and alkaline soils. Our results provide insight into how soil DOM affects the community structure and function of bacteria to regulate the process of nitrogen transformation in plant-soil system.
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Affiliation(s)
- Chang Zhao
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Xiaoxiang He
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Xiaoqian Dan
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Mengqiu He
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Jun Zhao
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource, Development and Application, Nanjing 210023, PR China
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing 210023, PR China.
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource, Development and Application, Nanjing 210023, PR China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China; Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, PR China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource, Development and Application, Nanjing 210023, PR China
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16
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Gangola S, Bhatt P, Kumar AJ, Bhandari G, Joshi S, Punetha A, Bhatt K, Rene ER. Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment. CHEMOSPHERE 2022; 296:133916. [PMID: 35149016 DOI: 10.1016/j.chemosphere.2022.133916] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/23/2021] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.
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Affiliation(s)
- Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, Uttarakhand, India
| | - Pankaj Bhatt
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, PR China.
| | | | - Geeta Bhandari
- Department of Biosciences, Swami Rama Himalayan University, Dehradun, Uttarakhand, India
| | - Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, 263136, Uttarakhand, India
| | - Arjita Punetha
- Department of Environmental Science, GB Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, 249404, Uttarakhand, India
| | - Eldon R Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, P. O. Box 3015, 2601 DA Delft, the Netherlands
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17
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Ma Q, Kong D, Zhang Q, Li M, Han X, Che J, Zhou Y, Zhang W, Jiang X, Ruan Z. Microbacterium sulfonylureivorans sp. nov., isolated from sulfonylurea herbicides degrading consortium. Arch Microbiol 2022; 204:136. [DOI: 10.1007/s00203-021-02750-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 11/02/2022]
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18
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Wu X, Cai W, Zhu P, Peng Z, Zheng T, Li D, Li J, Zhou G, Zhang J, Du G. Function-driven design of Bacillus kochii and Filobasidium magnum co-culture to improve quality of flue-cured tobacco. Front Microbiol 2022; 13:1024005. [PMID: 36875537 PMCID: PMC9978371 DOI: 10.3389/fmicb.2022.1024005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/16/2022] [Indexed: 02/18/2023] Open
Abstract
Flue-cured tobacco (FCT) is an economical raw material whose quality affects the quality and cost of the derived product. However, the time-consuming and inefficient spontaneous aging is the primary process for improving the FCT quality in the industry. In this study, a function-driven co-culture with functional microorganisms was built in response to the quality-driven need for less irritation and more aroma in FCT. The previous study has found that Bacillus kochii SC could degrade starch and protein to reduce tobacco irritation and off-flavors. The Filobasidium magnum F7 with high lipoxygenase activity was screened out for degrading higher fatty acid esters and terpenoids to promote the aroma and flavor of FCT. Co-cultivation with strain SC and F7 obtained better quality improvement than mono-culture at an initial inoculation ratio of 1:3 for 2 days, representing a significant breakthrough in efficiency and a reduction in production costs compared to the more than 2 years required for the spontaneous aging process. Through the analysis of microbial diversity, predicted flora functions, enzyme activities and volatile compositions within the mono- and co-cultivation, our study showed the formation of a function-driven co-culture between two strains through functional division of labor and nutritional feeding. Herein, the function-driven co-culture via bioaugmentation will become an increasingly implemented approach for the tobacco industry.
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Affiliation(s)
- Xinying Wu
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China.,School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Wen Cai
- Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., Chengdu, China
| | - Pengcheng Zhu
- School of Biotechnology, Jiangnan University, Wuxi, China.,Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., Chengdu, China
| | - Zheng Peng
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Tianfei Zheng
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Dongliang Li
- Technical Research Center, China Tobacco Sichuan Industrial Co., Ltd., Chengdu, China
| | - Jianghua Li
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Guanyu Zhou
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Juan Zhang
- School of Biotechnology, Jiangnan University, Wuxi, China.,Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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19
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de Oliveira EP, Rovida AFDS, Martins JG, Pileggi SAV, Schemczssen-Graeff Z, Pileggi M. Tolerance of Pseudomonas strain to the 2,4-D herbicide through a peroxidase system. PLoS One 2021; 16:e0257263. [PMID: 34855750 PMCID: PMC8638965 DOI: 10.1371/journal.pone.0257263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/16/2021] [Indexed: 01/22/2023] Open
Abstract
Herbicides are widely used in agricultural practices for preventing the proliferation of weeds. Upon reaching soil and water, herbicides can harm nontarget organisms, such as bacteria, which need an efficient defense mechanism to tolerate stress induced by herbicides. 2,4-Dichlorophenoxyacetic acid (2,4-D) is a herbicide that exerts increased oxidative stress among bacterial communities. Bacterial isolates were obtained from the biofilm of tanks containing washing water from the packaging of different pesticides, including 2,4-D. The Pseudomonas sp. CMA-7.3 was selected because of its tolerance against 2,4-D toxicity, among several sensitive isolates from the biofilm collection. This study aimed to evaluate the antioxidative response system of the selected strain to 2,4-D. It was analyzed the activity of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and guaiacol peroxidase GPX enzymes, that are poorly known in the literature for bacterial systems. The Pseudomonas sp. CMA-7.3 presented an efficient response system in balancing the production of hydrogen peroxide, even at 25x the dose of 2,4-D used in agriculture. The antioxidative system was composed of Fe–SOD enzymes, less common than Mn–SOD in bacteria, and through the activities of KatA and KatB isoforms, working together with APX and GPX, having their activities coordinated possibly by quorum sensing molecules. The peroxide control is poorly documented for bacteria, and this work is unprecedented for Pseudomonas and 2,4-D. Not all bacteria harbor efficient response system to herbicides, therefore they could affect the diversity and functionality of microbiome in contaminated soils, thereby impacting agricultural production, environment sustainability and human health.
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Affiliation(s)
- Elizangela Paz de Oliveira
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Juliane Gabriele Martins
- Departamento de Biologia Estrutural e Molecular e Genética, Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Sônia Alvim Veiga Pileggi
- Departamento de Biologia Estrutural e Molecular e Genética, Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | | | - Marcos Pileggi
- Departamento de Biologia Estrutural e Molecular e Genética, Laboratório de Microbiologia Ambiental, Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
- * E-mail:
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20
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Biodegradation and metabolic pathway of sulfamethoxazole by Sphingobacterium mizutaii. Sci Rep 2021; 11:23130. [PMID: 34848765 PMCID: PMC8632973 DOI: 10.1038/s41598-021-02404-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 11/24/2022] Open
Abstract
Sulfamethoxazole (SMX) is the most commonly used antibiotic in worldwide for inhibiting aquatic animal diseases. However, the residues of SMX are difficult to eliminate and may enter the food chain, leading to considerable threats on human health. The bacterial strain Sphingobacterium mizutaii LLE5 was isolated from activated sludge. This strain could utilize SMX as its sole carbon source and degrade it efficiently. Under optimal degradation conditions (30.8 °C, pH 7.2, and inoculum amount of 3.5 × 107 cfu/mL), S. mizutaii LLE5 could degrade 93.87% of 50 mg/L SMX within 7 days. Four intermediate products from the degradation of SMX were identified and a possible degradation pathway based on these findings was proposed. Furthermore, S. mizutaii LLE5 could also degrade other sulfonamides. This study is the first report on (1) degradation of SMX and other sulfonamides by S. mizutaii, (2) optimization of biodegradation conditions via response surface methodology, and (3) identification of sulfanilamide, 4-aminothiophenol, 5-amino-3-methylisoxazole, and aniline as metabolites in the degradation pathway of SMX in a microorganism. This strain might be useful for the bioremediation of SMX-contaminated environment.
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Rovida AFDS, Costa G, Santos MI, Silva CR, Freitas PNN, Oliveira EP, Pileggi SAV, Olchanheski RL, Pileggi M. Herbicides Tolerance in a Pseudomonas Strain Is Associated With Metabolic Plasticity of Antioxidative Enzymes Regardless of Selection. Front Microbiol 2021; 12:673211. [PMID: 34239509 PMCID: PMC8258386 DOI: 10.3389/fmicb.2021.673211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022] Open
Abstract
Agriculture uses many food production chains, and herbicides participate in this process by eliminating weeds through different biochemical strategies. However, herbicides can affect non-target organisms such as bacteria, which can suffer damage if there is no efficient control of reactive oxygen species. It is not clear, according to the literature, whether the efficiency of this control needs to be selected by the presence of xenobiotics. Thus, the Pseudomonas sp. CMA 6.9 strain, collected from biofilms in an herbicide packaging washing tank, was selected for its tolerance to pesticides and analyzed for activities of different antioxidative enzymes against the herbicides Boral®, absent at the isolation site, and Heat®, present at the site; both herbicides have the same mode of action, the inhibition of the enzyme protoporphyrinogen oxidase. The strain showed tolerance to both herbicides in doses up to 45 times than those applied in agriculture. The toxicity of these herbicides, which is greater for Boral®, was assessed by means of oxidative stress indicators, growth kinetics, viability, and amounts of peroxide and malondialdehyde. However, the studied strain showed two characteristic antioxidant response systems for each herbicide: glutathione-s-transferase acting to control malondialdehyde in treatments with Boral®; and catalase, ascorbate peroxidase, and guaiacol peroxidase in the control of peroxide induced by Heat®. It is possible that this modulation of the activity of different enzymes independent of previous selection characterizes a system of metabolic plasticity that may be more general in the adaptation of microorganisms in soil and water environments subjected to chemical contaminants. This is relevant to the impact of pesticides on the diversity and abundance of microbial species as well as a promising line of metabolic studies in microbial consortia for use in bioremediation.
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Affiliation(s)
| | - Gessica Costa
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Mariana Inglês Santos
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Caroline Rosa Silva
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Paloma Nathane Nunes Freitas
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Elizangela Paz Oliveira
- Department of Biotechnology, Genetics and Cell Biology, State University of Maringá, Maringá, Brazil
| | - Sônia Alvim Veiga Pileggi
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Ricardo Luiz Olchanheski
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Marcos Pileggi
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
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Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang Q. Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium. Int J Syst Evol Microbiol 2021; 71. [PMID: 33411665 DOI: 10.1099/ijsem.0.004632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902T, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902T were 30 °C and pH 6.0, respectively. Strain LAM1902T could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902T was closely related to the members of the family Pseudomonadaceae to the genus Pseudomonas, with the highest similarity to Pseudomonas nitroreducens DSM 14399T (99.6 %), Pseudomonas nitritireducens WZBFD3-5A2T (99.3 %) and Pseudomonas panipatensis Esp-1T (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (gyrB, rpoB and rpoD) further confirmed the intrageneric phylogenetic position of strain LAM1902T. The genomic DNA G+C content of LAM1902T was 64.8 mol%. The low values of in silico DNA-DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus Pseudomonas. The major fatty acids were C16 : 0, C17 : 0 cyclo and anteiso C15 : 0. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902T represents a novel species, for which the name Pseudomonas nicosulfuronedens sp. nov. is proposed. The type strain is LAM1902T (=JCM 33860T=KCTC 72830T).
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Affiliation(s)
- Miaomiao Li
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qingyun Ma
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xiaoyan Han
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Juan Che
- College of Life Science, Xinjiang Normal University, Urumqi, XinJiang, 830046, PR China.,Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Xu Jiang
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China.,College of Resources and Environment, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, Tibet, PR China
| | - Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China
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Wen T, Yuan J, He X, Lin Y, Huang Q, Shen Q. Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion. HORTICULTURE RESEARCH 2020; 7:154. [PMID: 33082961 PMCID: PMC7527982 DOI: 10.1038/s41438-020-00380-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/05/2020] [Accepted: 07/10/2020] [Indexed: 05/16/2023]
Abstract
Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae, a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be "cultured" by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.
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Affiliation(s)
- Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong, China
| | - Yue Lin
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095 Nanjing, China
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Wen T, Zhao M, Liu T, Huang Q, Yuan J, Shen Q. High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome. BMC PLANT BIOLOGY 2020; 20:166. [PMID: 32293273 PMCID: PMC7160980 DOI: 10.1186/s12870-020-02365-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology. RESULTS There is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance. CONCLUSIONS The dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability.
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Affiliation(s)
- Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
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