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Wong MH, Minkina T, Vasilchenko N, Sushkova S, Delegan Y, Ranjan A, Saxena P, Tarigholizadeh S, Dudnikova T, Barbashev A, Maksimov A, Faenson A, Kızılkaya R. Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals. ENVIRONMENTAL RESEARCH 2024; 252:118949. [PMID: 38631472 DOI: 10.1016/j.envres.2024.118949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/18/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.
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Affiliation(s)
- Ming Hung Wong
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia; Consortium on Health, Environment, Education, and Research (CHEER), The Educaiton University of Hong Kong, Tai Po, Hong Kong, China
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Nikita Vasilchenko
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia; Almetyevsk State Oil Institute, 423450 Almetyevsk, Republic of Tatarstan, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Yanina Delegan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino, 142290 Moscow, Russia
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia.
| | - Pallavi Saxena
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Sarieh Tarigholizadeh
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Tamara Dudnikova
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Andrey Barbashev
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Aleksey Maksimov
- National Medical Research Centre for Oncology, 344037 Rostov-on-Don, Russia
| | - Alexandr Faenson
- National Medical Research Centre for Oncology, 344037 Rostov-on-Don, Russia
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2
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Li K, Zhu Y, Shi X, Yan M, Li J, Zhang W, Shao Y, Shao Y. Effects of Zn and oxytetracycline on mobile genetic elements, antibiotic resistance genes, and microbial community evolution in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122609. [PMID: 37742856 DOI: 10.1016/j.envpol.2023.122609] [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: 08/12/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
Antibiotics and heavy metals added to livestock and poultry feed are excreted in manure, which is added to agricultural soil and causes severe pollution. However, the effects of oxytetracycline (OTC) and zinc (Zn), which are present at relatively high levels in feed additives, on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial communities have not been comprehensively studied. This study evaluated the effects of OTC and Zn on environmental factors, microorganisms, MGEs, and ARGs. The expression of MGEs in soil was stimulated by adding Zn at concentrations of 500 and 1000 mg/kg or OTC at concentrations of 30 and 100 mg/kg; however, the addition of their combination hindered the expression of MGEs in soil. The abundance of total MGEs and ARGs tended to decrease with increasing concentrations of Zn and OTC and the number of incubation days. Low and high OTC concentrations strongly inhibited sul and tet resistance genes, respectively. Network analysis showed that changes in the population of Firmicutes and Proteobacteria had the greatest impact on ARG abundance. Redundancy analysis revealed that MGEs, particularly intI2, facilitated the transfer and spread of ARGs and had the greatest impact on changes in ARG abundance. These findings provide reference values for the prevention and resolution of ecological and environmental risks posed by the presence of Zn and OTC in organic manure soil.
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Affiliation(s)
- Ke Li
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Ying Zhu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xinhua Shi
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Maolu Yan
- Shandong Ecological Home Environmental Protection Co., LTD, Jinan, 250000, China
| | - Jing Li
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Weiyi Zhang
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Yingying Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Yanqiu Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China.
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Zhang H, Shen T, Tang J, Ling H, Wu X. Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress. ENVIRONMENT INTERNATIONAL 2023; 182:108318. [PMID: 37984292 DOI: 10.1016/j.envint.2023.108318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Tiantian Shen
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Hong Ling
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China.
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Chen X, Zheng X, Fu W, Liu A, Wang W, Wang G, Ji J, Guan C. Microplastics reduced bioavailability and altered toxicity of phenanthrene to maize (Zea mays L.) through modulating rhizosphere microbial community and maize growth. CHEMOSPHERE 2023; 345:140444. [PMID: 37839745 DOI: 10.1016/j.chemosphere.2023.140444] [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: 02/21/2023] [Revised: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Due to its large specific surface area and great hydrophobicity, microplastics can adsorb polycyclic aromatic hydrocarbons (PAHs), affecting the bioavailability and the toxicity of PAHs to plants. This study aimed to evaluate the effects of D550 and D250 (with diameters of 550 μm and 250 μm) microplastics on phenanthrene (PHE) removal from soil and PHE accumulation in maize (Zea mays L.). Moreover, the effects of microplastics on rhizosphere microbial community of maize grown in PHE-contaminated soil would also be determined. The results showed that D550 and D250 microplastics decreased the removal of PHE from soil by 6.5% and 2.7% and significantly reduced the accumulation of PHE in maize leaves by 64.9% and 88.5%. Interestingly, D550 microplastics promoted the growth of maize and enhanced the activities of soil protease and alkaline phosphatase, while D250 microplastics significantly inhibited the growth of maize and decreased the activities of soil invertase, alkaline phosphatase and catalase, in comparison with PHE treatment. In addition, microplastics changed the rhizosphere soil microbial community and reduced the relative abundance of PAHs degrading bacteria (Pseudomonas, Massilia, Proteobacteria), which might further inhibit the removal of PHE from soil. This study provided a new perspective for evaluating the role of microplastics on the bioavailability of PHE to plants and revealing the combined toxicity of microplastics and PHE to soil microcosm and plant growth.
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Affiliation(s)
- Xiancao Chen
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Xiaoyan Zheng
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Wenting Fu
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Anran Liu
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Wenjing Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Gang Wang
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Jing Ji
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
| | - Chunfeng Guan
- School of Environmental Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, China.
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Liu S, Xu Q, Lou S, Tu J, Yin W, Li X, Jin Y, Radnaeva LD, Nikitina E, Makhinov AN, Araruna JT, Fedorova IV. Spatiotemporal distributions of sulfonamide and tetracycline resistance genes and microbial communities in the coastal areas of the Yangtze River Estuary. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115025. [PMID: 37216861 DOI: 10.1016/j.ecoenv.2023.115025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 05/24/2023]
Abstract
In this paper, water and sediments were sampled at eight monitoring stations in the coastal areas of the Yangtze River Estuary in summer and autumn 2021. Two sulfonamide resistance genes (sul1 and sul2), six tetracycline resistance genes (tetM, tetC, tetX, tetA, tetO, and tetQ), one integrase gene (intI1), 16 S rRNA genes, and microbial communities were examined and analyzed. Most resistance genes showed relatively higher abundance in summer and lower abundance in autumn. One-way analysis of variance (ANOVA) showed significant seasonal variation of some ARGs (7 ARGs in water and 6 ARGs in sediment). River runoff and WWTPs are proven to be the major sources of resistance genes along the Yangtze River Estuary. Significant and positive correlations between intI1 and other ARGs were found in water samples (P < 0.05), implying that intI1 may influence the spread and propagation of resistance genes in aquatic environments. Proteobacteria was the dominant phylum along the Yangtze River Estuary, with an average proportion of 41.7%. Redundancy analysis indicated that the ARGs were greatly affected by temperature, dissolved oxygen, and pH in estuarine environments. Network analysis showed that Proteobacteria and Cyanobacteria were the potential host phyla for ARGs in the coastal areas of the Yangtze River Estuary.
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Affiliation(s)
- Shuguang Liu
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China; Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, China
| | - Qiuhong Xu
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
| | - Sha Lou
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China; Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, China.
| | - Junbiao Tu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Wenjun Yin
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Xin Li
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
| | - Yuchen Jin
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
| | - Larisa Dorzhievna Radnaeva
- Laboratory of Chemistry of Natural Systems, Baikal Institute of Nature Management of Siberian Branch of the Russian Academy of Sciences, Republic of Buryatia, Russian Republic, Russia
| | - Elena Nikitina
- Laboratory of Chemistry of Natural Systems, Baikal Institute of Nature Management of Siberian Branch of the Russian Academy of Sciences, Republic of Buryatia, Russian Republic, Russia
| | | | | | - Irina Viktorovna Fedorova
- Institute of Earth Sciences, Saint Petersburg State University, 7-9 Universitetskaya Embankment, St Petersburg, Russia
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6
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Li YQ, Xin Y, Li C, Liu J, Huang T. Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil. Braz J Microbiol 2023:10.1007/s42770-023-01000-7. [PMID: 37162704 DOI: 10.1007/s42770-023-01000-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.
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Affiliation(s)
- Yong-Quan Li
- School of Medicine, Northwest Minzu University, Lanzhou, China.
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, State Ethnic Affairs Commission, Lanzhou, China.
| | - Ying Xin
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Caili Li
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Jin Liu
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Tao Huang
- School of Medicine, Northwest Minzu University, Lanzhou, China
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7
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Yang R, Zhou S, Zhang L, Qin C. Pronounced temporal changes in soil microbial community and nitrogen transformation caused by benzalkonium chloride. J Environ Sci (China) 2023; 126:827-835. [PMID: 36503808 PMCID: PMC9553405 DOI: 10.1016/j.jes.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 05/16/2023]
Abstract
As one typical cationic disinfectant, quaternary ammonium compounds (QACs) were approved for surface disinfection in the coronavirus disease 2019 pandemic and then unintentionally or intentionally released into the surrounding environment. Concerningly, it is still unclear how the soil microbial community succession happens and the nitrogen (N) cycling processes alter when exposed to QACs. In this study, one common QAC (benzalkonium chloride (BAC) was selected as the target contaminant, and its effects on the temporal changes in soil microbial community structure and nitrogen transformation processes were determined by qPCR and 16S rRNA sequencing-based methods. The results showed that the aerobic microbial degradation of BAC in the two different soils followed first-order kinetics with a half-life (4.92 vs. 17.33 days) highly dependent on the properties of the soil. BAC activated the abundance of N fixation gene (nifH) and nitrification genes (AOA and AOB) in the soil and inhibited that of denitrification gene (narG). BAC exposure resulted in the decrease of the alpha diversity of soil microbial community and the enrichment of Crenarchaeota and Proteobacteria. This study demonstrates that BAC degradation is accompanied by changes in soil microbial community structure and N transformation capacity.
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Affiliation(s)
- Rui Yang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Shaohong Zhou
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Cunli Qin
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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8
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Tang Z, Zhang Y, Xiao S, Gao Y, Duan Y, Liu B, Xiong C, Yang Z, Wu Y, Zhou S. Insight into the impacts and mechanisms of ketone stress on the antibiotic resistance in Escherichia coli. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:83746-83755. [PMID: 35771331 PMCID: PMC9245865 DOI: 10.1007/s11356-022-21600-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Accumulation of toxic organic has posed a substantial pressure on the proliferation of bacterial resistance. While aromatic organics have been demonstrated to enhance the antibiotic resistance in bacteria, no information is yet available on the effects of non-aromatic organics on the variations of bacterial resistance. Here, we investigated the effects of a typical ketone (i.e., methylisobutanone (MIBK)) on the variations of antibiotic resistance in Escherichia coli (E. coli). The results showed that the growth of resistant E. coli under environmental concentration of 50 μg/L MIBK was firstly inhibited as explained by the transient disruption in the cell membrane and then recovered possibly due to the reactive oxygen species. Exposure to 50 μg/L MIBK gradually raised the abundance of representative resistance gene (ampR) in E. coli. In contrast, the high concentration of 50 mg/L MIBK continuously inhibited the growth of resistant E. coli by disrupting cell membrane and notably promoted the proliferation of ampR through enhancing the horizontal transformation and up-regulating the expression of efflux pump gene. These findings provided the first evidence for the evolution of bacterial resistance in response to ketone organics.
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Affiliation(s)
- Zhenping Tang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Yu Zhang
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Shasha Xiao
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yuanyuan Gao
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Yi Duan
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Boyang Liu
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Cong Xiong
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Zhengqing Yang
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yueyue Wu
- Institute of Pathogenic Biology, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Shuai Zhou
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China.
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China.
- School of Civil Engineering, University of South China, Hengyang, 421001, China.
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Liu X, He L, Zhang X, Kong D, Chen Z, Lin J, Wang C. Bioremediation of petroleum-contaminated saline soil by Acinetobacter baumannii and Talaromyces sp. and functional potential analysis using metagenomic sequencing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119970. [PMID: 35995289 DOI: 10.1016/j.envpol.2022.119970] [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: 05/18/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Microbial remediation is a potential remediation method for petroleum-contaminated soil. In order to explore the petroleum degradation mechanism by microorganisms, the oilfield soil was remedied by Acinetobacter baumannii combined with Talaromyces sp. The degradation mechanism was studied by analyzing soil microbial community and functional genes through metagenomics during the degradation process. The result showed the degradation rate of petroleum was 65.6% after 28 days. The concentration of petroleum decreased from 1220 mg/kg to 420 mg/kg. In the co-culture group, Acinetobacter baumannii became the dominant species, the annotated genes of it at the species level accounted for 7.34% while that of Talaromyces sp. accounted for only 0.34%. Meanwhile, the annotated genes of Bacillus, Halomonas, and Nitriliruptor at the genus level were up-regulated by 1.83%, 0.90%, and 0.71%, respectively. In addition, large functional genes were significantly up-regulated, including the peroxisome, P450 enzyme (CYP53, CYP116, CYP102, CYP645), and biofilm formulation, promoting the oxidation and hydroxylation, and catalyzing the epoxidation of aromatic and aliphatic hydrocarbons. Meanwhile, the degrading genes of alkanes and aromatic hydrocarbons were expressed promotionally, and degradation pathways were deduced. In conclusion, the inoculation of Acinetobacter baumannii combined with Talaromyces sp. accelerated the degradation of petroleum in oilfield soil and improved the growth of indigenous petroleum-degrading bacteria. Many functional genes related to petroleum degradation were promoted significantly. These results proved the co-culture of bacteria-fungi consortium contributes to the bioremediation of petroleum-contaminated soil.
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Affiliation(s)
- Xiaoyan Liu
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Lihong He
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Xinying Zhang
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Dewen Kong
- Shanghai Solid Waste Disposal Co., Ltd., No. 666, Lane 2088, Nanbin Highway, Shanghai, 201302, China
| | - Zongze Chen
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Jia Lin
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Chuanhua Wang
- College of Life and Environment Science, Wenzhou University, Wenzhou, Zhejiang, 325035, China
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10
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Miral A, Kautsky A, Alves-Carvalho S, Cottret L, Guillerm-Erckelboudt AY, Buguet M, Rouaud I, Tranchimand S, Tomasi S, Bartoli C. Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance. Microorganisms 2022; 10:1859. [PMID: 36144461 PMCID: PMC9503503 DOI: 10.3390/microorganisms10091859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.
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Affiliation(s)
- Alice Miral
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Adam Kautsky
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Susete Alves-Carvalho
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Ludovic Cottret
- CNRS, Université de Toulouse, 31320 Castanet-Tolosan, France
| | | | - Manon Buguet
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Isabelle Rouaud
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sylvain Tranchimand
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sophie Tomasi
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Claudia Bartoli
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
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11
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Kaviani Rad A, Balasundram SK, Azizi S, Afsharyzad Y, Zarei M, Etesami H, Shamshiri RR. An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084666. [PMID: 35457533 PMCID: PMC9025980 DOI: 10.3390/ijerph19084666] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/29/2023]
Abstract
Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR’s negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.
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Affiliation(s)
- Abdullah Kaviani Rad
- Department of Soil Science, School of Agriculture, Shiraz University, Shiraz 71946-85111, Iran;
| | - Siva K. Balasundram
- Department of Agriculture Technology, Faculty of Agriculture, University Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: (S.K.B.); (M.Z.)
| | - Shohreh Azizi
- UNESCO-UNISA Africa Chair in Nanosciences and Nanotechnology, College of Graduate Studies, University of South Africa, Pretoria 0003, South Africa;
- Nanosciences African Network (NANOAFNET), iThemba LABS-National Research Foundation, Cape Town 7129, South Africa
| | - Yeganeh Afsharyzad
- Department of Microbiology, Faculty of Modern Sciences, The Islamic Azad University of Tehran Medical Sciences, Tehran 19496-35881, Iran;
| | - Mehdi Zarei
- Department of Soil Science, School of Agriculture, Shiraz University, Shiraz 71946-85111, Iran;
- Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid 73819-43885, Iran
- Correspondence: (S.K.B.); (M.Z.)
| | - Hassan Etesami
- Department of Soil Science, University of Tehran, Tehran 14179-35840, Iran;
| | - Redmond R. Shamshiri
- Leibniz Institute for Agricultural Engineering and Bioeconomy, 14469 Potsdam-Bornim, Germany;
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12
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Yi M, Zhang L, Qin C, Lu P, Bai H, Han X, Yuan S. Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene. CHEMOSPHERE 2022; 286:131709. [PMID: 34340117 DOI: 10.1016/j.chemosphere.2021.131709] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.
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Affiliation(s)
- Meiling Yi
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lilan Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Cunli Qin
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Peili Lu
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Hongcheng Bai
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Xinkuan Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shupei Yuan
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
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13
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Maurya AP, Rajkumari J, Pandey P. Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:12178-12189. [PMID: 33394421 DOI: 10.1007/s11356-020-12171-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.
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Affiliation(s)
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
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