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Guo X, Zhao W, Yin D, Mei Z, Wang F, Tiedje J, Ling S, Hu S, Xu T. Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124566. [PMID: 39025292 DOI: 10.1016/j.envpol.2024.124566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.
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Affiliation(s)
- Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Wanting Zhao
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Siyuan Ling
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Shuangqing Hu
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Ting Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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2
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Fu Y, Hu F, Wang F, Xu M, Jia Z, Amelung W, Mei Z, Han X, Virta M, Jiang X, Tiedje JM. Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10216-10226. [PMID: 38802328 DOI: 10.1021/acs.est.3c10423] [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: 05/29/2024]
Abstract
Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.
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Affiliation(s)
- Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Chongqing Changan Automobile Co., Ltd., Chongqing 400023, China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjun Jia
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun130102,China
| | - Wulf Amelung
- Agrosphere institute (IBG-3), Forschungszentrum Jülich GmbH, 52428Jülich ,Germany
- Institute of Crop Science and Resource Conservation (INRES)-Soil Science and Soil Ecology, University of Bonn, 53113Bonn, Germany
| | - Zhi Mei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014Helsinki,Finland
| | - Xiaozeng Han
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014Helsinki,Finland
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
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3
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Fu Y, Jia F, Su J, Xu X, Zhang Y, Li X, Jiang X, Schäffer A, Virta M, Tiedje JM, Wang F. Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134252. [PMID: 38657507 DOI: 10.1016/j.jhazmat.2024.134252] [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: 08/29/2023] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.
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Affiliation(s)
- Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feiran Jia
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Jingfang Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xinyao Xu
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Yuqin Zhang
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andreas Schäffer
- Institute for Environmental Research, RWTH Aachen University, Aachen 52074, Germany
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Environmental Research, RWTH Aachen University, Aachen 52074, Germany.
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Durán-Viseras A, Lindner BG, Hatt JK, Lai A, Wallace R, Ginn O, Brown J, Konstantinidis KT. Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170772. [PMID: 38346660 DOI: 10.1016/j.scitotenv.2024.170772] [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: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla 41012, Spain; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amanda Lai
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Robert Wallace
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olivia Ginn
- Chemical, Materials and Biomedical Engineering Department and Institute for Bioinformatics, University of Georgia, Athens, GA 30601, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Xue W, Shi X, Guo J, Wen S, Lin W, He Q, Gao Y, Wang R, Xu Y. Affecting factors and mechanism of removing antibiotics and antibiotic resistance genes by nano zero-valent iron (nZVI) and modified nZVI: A critical review. WATER RESEARCH 2024; 253:121309. [PMID: 38367381 DOI: 10.1016/j.watres.2024.121309] [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: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
Antibiotics and antibiotic resistance genetic pollution have become a global environmental and health concern recently, with frequent detection in various environmental media. Therefore, finding ways to control antibiotics and antibiotic resistance genes (ARGs) is urgently needed. Nano zero-valent iron (nZVI) has shown a positive effect on antibiotics degradation and restraining ARGs, making it a promising solution for controlling antibiotics and ARGs. However, given the current increasingly fragmented research focus and results, a comprehensive review is still lacking. In this work, we first introduce the origin and transmission of antibiotics and ARGs in various environmental media, and then discuss the affecting factors during the degradation of antibiotics and the control of ARGs by nZVI and modified nZVI, including pH, nZVI dose, and oxidant concentration, etc. Then, the mechanisms of antibiotic and ARGs removal promoted by nZVI are also summarized. In general, the mechanism of antibiotic degradation by nZVI mainly includes adsorption and reduction, while promoting the biodegradation of antibiotics by affecting the microbial community. nZVI can also be combined with persulfates to degrade antibiotics through advanced oxidation processes. For the control of ARGs, nZVI not only changes the microbial community structure, but also affects the proliferation of ARGs through affecting the fate of mobile genetic elements (MGEs). Finally, some new ideas on the application of nZVI in the treatment of antibiotic resistance are proposed. This paper provides a reference for research and application in this field.
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Affiliation(s)
- Wenjing Xue
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaoyu Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Jiaming Guo
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Siqi Wen
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Weilong Lin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Qi He
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Yang Gao
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, PR China
| | - Rongzhong Wang
- School of Resource & Environment and Safety Engineering, University of South China, Heng yang 421001, PR China
| | - Yiqun Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China.
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Zhang J, Lu K, Zhu L, Li N, Lin D, Cheng Y, Wang M. Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133272. [PMID: 38134686 DOI: 10.1016/j.jhazmat.2023.133272] [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: 08/02/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.
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Affiliation(s)
- Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Kun Lu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Na Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yangjuan Cheng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China.
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Ni B, Zhang TL, Cai TG, Xiang Q, Zhu D. Effects of heavy metal and disinfectant on antibiotic resistance genes and virulence factor genes in the plastisphere from diverse soil ecosystems. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133335. [PMID: 38142651 DOI: 10.1016/j.jhazmat.2023.133335] [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: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Antibiotic-resistance genes (ARGs) are world-wide contaminants posing potential health risks. Quaternary ammonium compounds (QACs) and heavy metals can apply selective pressure on antibiotic resistance. However, there is a lack of evidence regarding their coupled effect on changes in ARGs and virulence factor genes (VFGs) in various soil types and their plastispheres. Herein, we conducted a microcosm experiment to explore the abundances and profiles of ARGs and VFGs in soil plastispheres from three distinct types of soils amended with Cu and disinfectants. The plastispheres enriched the ARGs' abundance compared to soils and stimulated the coupling effect of combined pollutants on promoting the abundances of ARGs and VFGs. Horizontal gene transfer inevitably accelerates the propagation of ARGs and VFGs in plastispheres under pollutant stress. In plastispheres, combined exposure to disinfectants and Cu increased some potential pathogens' relative abundances. Moreover, the combined effect of disinfectants and Cu on ARGs and VFGs changed with soil type in plastispheres, emphasising the necessity to incorporate soil type considerations into health risk assessments for ARGs and VFGs. Overall, this study highlights the high health risks of ARGs under the selective pressure of combined pollutants in plastispheres and provides valuable insights for future risk assessments related to antibiotic resistance.
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Affiliation(s)
- Bang Ni
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Tian-Lun Zhang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tian-Gui Cai
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China.
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8
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Nkoh JN, Shang C, Okeke ES, Ejeromedoghene O, Oderinde O, Etafo NO, Mgbechidinma CL, Bakare OC, Meugang EF. Antibiotics soil-solution chemistry: A review of environmental behavior and uptake and transformation by plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120312. [PMID: 38340667 DOI: 10.1016/j.jenvman.2024.120312] [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: 07/22/2023] [Revised: 10/21/2023] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
The increased use of antibiotics by humans for various purposes has left the environment polluted. Antibiotic pollution remediation is challenging because antibiotics exist in trace amounts and only highly sensitive detection techniques could be used to quantify them. Nevertheless, their trace quantity is not a hindrance to their transfer along the food chain, causing sensitization and the development of antibiotic resistance. Despite an increase in the literature on antibiotic pollution and the development and transfer of antibiotic-resistant genes (ARGs), little attention has been given to the behavior of antibiotics at the soil-solution interface and how this affects antibiotic adsorption-desorption interactions and subsequent uptake and transformation by plants. Thus, this review critically examines the interactions and possible degradation mechanisms of antibiotics in soil and the link between antibiotic soil-solution chemistry and uptake by plants. Also, different factors influencing antibiotic mobility in soil and the transfer of ARGs from one organism to another were considered. The mechanistic and critical analyses revealed that: (a) the charge characteristics of antibiotics at the soil-root interface determine whether they are adsorbed to soil or taken up by plants; (b) antibiotics that avoid soil colloids and reach soil pore water can be absorbed by plant roots, but their translocation to the stem and leaves depends on the ionic state of the molecule; (c) few studies have explored how plants adapt to antibiotic pollution and the transformation of antibiotics in plants; and (d) the persistence of antibiotics in cropland soils can be influenced by the content of soil organic matter, coexisting ions, and fertilization practices. Future research should focus on the soil/solution-antibiotic-plant interactions to reveal detailed mechanisms of antibiotic transformation by plants and whether plant-transformed antibiotics could be of environmental risk.
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Affiliation(s)
- Jackson Nkoh Nkoh
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Department of Chemistry, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Chenjing Shang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Emmanuel Sunday Okeke
- Organization of African Academic Doctors (OAAD), Off Kamiti Road, P. O. Box 25305000100, Nairobi, Kenya; Department of Biochemistry, Faculty of Biological Science University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013 China.
| | - Onome Ejeromedoghene
- Organization of African Academic Doctors (OAAD), Off Kamiti Road, P. O. Box 25305000100, Nairobi, Kenya; School of Chemistry and Chemical Engineering, Southeast University, Jiangning District, Nanjing, Jiangsu Province, 211189, China
| | - Olayinka Oderinde
- Department of Chemistry, Faculty of Natural and Applied Sciences, Lead City University, Ibadan, Nigeria
| | - Nelson Oshogwue Etafo
- Programa de Posgrado en Ciencia y Tecnología de Materiales, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing. J. Cárdenas Valdez S/N Republica, 25280 Saltillo, Coahuila Mexico
| | - Chiamaka Linda Mgbechidinma
- Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Department of Microbiology, University of Ibadan, Ibadan, Oyo State, 200243, Nigeria
| | - Omonike Christianah Bakare
- Department of Biological Sciences, Faculty of Natural and Applied Sciences, Lead City University, Ibadan, Nigeria
| | - Elvira Foka Meugang
- School of Metallurgy & Environment, Central South University, 932 Lushan South Road, Changsha, 410083, China
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9
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Li X, Zhu L, Zhang SY, Li J, Lin D, Wang M. Characterization of microbial contamination in agricultural soil: A public health perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169139. [PMID: 38070547 DOI: 10.1016/j.scitotenv.2023.169139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Soil is widely recognized as a reservoir of microbial contaminants including antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), which are major public health concerns. Although the risks associated with soil safety in different soil habitats have been studied, the results are not comprehensive. In this study, dryland soils used for vegetable, corn, and soybean planting, and submerged soils used for rice planting and crab farming were collected and subjected to metagenomic sequencing to characterize HBPs, ARGs, and virulence factor genes (VFGs). The results showed that submerged soils had a higher abundance of HBP than dryland soils. In addition, the submerged soil microbiome acquired significantly higher levels of high-risk ARGs than the dryland soil microbiome and these ARGs were mainly assigned to bacA, sul1, and aadA genes submerged. Network analysis revealed that 11 HBPs, including Yersinia enterocolitica, Vibrio cholerae, Escherichia coli, and Leptospira interrogans, were high-risk because of their close association with ARGs, VFGs, and mobile genetic elements (MGEs). Procrustes and network analyses showed that HBPs and ARGs were more closely linked in submerged soil. This study confirms that submerged field has higher ecological environment risk and human health risk than dryland soil.
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Affiliation(s)
- Xiaodi Li
- International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development & Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Lin Zhu
- International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development & Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Si-Yu Zhang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Jingpeng Li
- International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development & Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Da Lin
- International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development & Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Meizhen Wang
- International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development & Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
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10
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Zhang R, Gong C, Li J, Zhuang H, Lan L, Zhou L, Shan S, Wang Y. Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169181. [PMID: 38072280 DOI: 10.1016/j.scitotenv.2023.169181] [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: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.
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Affiliation(s)
- Ranran Zhang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China.
| | - Chenpan Gong
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Jimin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China
| | - Haifeng Zhuang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Lihua Lan
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Liuyuan Zhou
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China
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11
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Zhang M, Xu Y, Wang J, Hu J, Qi S, Jiang Z, Yang S. Impact of biochar on the antibiotic resistome and associated microbial functions in rhizosphere and bulk soil in water-saving and flooding irrigated paddy fields. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123026. [PMID: 38012968 DOI: 10.1016/j.envpol.2023.123026] [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: 09/08/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
The addition of biochar in paddies under the condition of water-saving irrigation can simultaneously achieve soil improvement and water conservation, but little is known about the role of these two regulations in mediating the fate of antibiotic resistome in paddy soils. Here, metagenomic analysis was conducted to investigate the effects and intrinsic mechanisms of biochar application and irrigation patterns on propagation of antibiotic resistance genes (ARGs) in paddy soils. The addition of biochar in paddy soil resulted in a reduction of approximately 1.32%-8.01% in the total absolute abundance of ARGs and 0.60%-22.09% in the numbers of ARG subtype. Compared with flooding irrigation, the numbers of detected ARG subtype were reduced by 1.60%-22.90%, but the total absolute abundance of ARGs increased by 0.06%-5.79% in water-saving irrigation paddy soils. Moreover, the combined treatments of flooding irrigation and biochar could significantly reduce the abundance of ARGs in paddy soils. The incremental antibiotic resistance in soil induced by water-saving irrigation was likewise mitigated by the addition of biochar. Correlation analyses indicated that, the differences in soil physicochemical properties under biochar addition or irrigation treatments contributed to the corresponding changes in the abundance of ARGs. Moreover, the variations of microbial community diversity, multidrug efflux abundance and transport system-related genes in paddy soil were also important for mediating the corresponding differences in the abundance of ARGs under the conditions of biochar addition or irrigation treatments. The findings of this study demonstrated the effectiveness of biochar application in mitigating antibiotic resistance in paddy soils. However, it also highlighted a potential concern relating to the elevated antibiotic resistance associated with water-saving irrigation in paddy fields. Consequently, these results contribute to a deeper comprehension of the environmental risks posed by ARGs in paddy soils.
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Affiliation(s)
- Mairan Zhang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China
| | - Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China
| | - Jie Wang
- Development Center for Science and Technology of Rural Water Resources of Jiangsu Province, Nanjing, 210029, China
| | - Jiazhen Hu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China
| | - Suting Qi
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China
| | - Zewei Jiang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China
| | - Shihong Yang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China; Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, 210098, China.
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12
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Liu Z, Jin Y, Yu Z, Liu Z, Zhang B, Chi T, Cheng D, Zhu L, Hu B. Vertical migration and dissipation of oxytetracycline induces the recoverable shift in microbial community and antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167162. [PMID: 37730066 DOI: 10.1016/j.scitotenv.2023.167162] [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: 06/12/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Antibiotic resistance gene (ARG) spread in anthropogenic polluted soils is believed to be accelerated by the incidental inputs of antibiotics via fertilizing and irrigation, and endangering food and human health. However, due to the complex nature of substrates and uncertain microbial responses, the primary drivers of ARG dissemination remain unclear. To address this concern, the effects of antibiotic inputs on soil microbes and antibiotic resistance under simulated natural conditions was investigated in this study. Specifically, four flow-through reactors with gravity flow were established, and the oxytetracycline (OTC) a typical antibiotic in agricultural soils was studied at environmental concentrations (i.e. 0.1, 1 and 10 mg/kg) for 31 days. The vertical distribution and dissipation of OTC were profiled by measuring the residuals in layers over time. Correspondingly, the effects of antibiotic exposure on microbial communities and ARG abundances were studied. The results showed that the average exposure intensity of OTC in different soil layers ranged in 0.03-6.45 mg/kg, and resulted in different dissipation kinetics. In addition, top layer was found to be the main site of OTC reduction, where OTC dissipated at magnitude of 74.0-96.6 %, depending on the initial OTC concentration. OTC migration and dissipation resulted in the shift of community composition to the extent of 0.25-0.33 in terms of Bray-Curtis distance, which partially recovered over time. And the achievement of alternative community compositions was supposed to be largely affected by the microbial interaction. Along with the community changes, a short-term accumulation of resistance genes was detected, while the relative abundance of indicator ARGs, i.e. tetG and mexB, rising up to 10-fold higher than the initial, although eventually decayed. Collective findings of this study indicated that antibiotics at environmental concentrations might trigger extra microbial interactions and thereby reducing the demand for ARGs accumulation. It provided valuable understandings in the risk of antibiotic spillage, especially for the incident exposure at the environmentally relevant concentrations.
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Affiliation(s)
- Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Yihao Jin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhendi Yu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Zhengzheng Liu
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Ecological and Environmental Monitoring Center, Hangzhou 310012, China.
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou 310007, China.
| | - Taolue Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310058, China.
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13
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Męcik M, Buta-Hubeny M, Paukszto Ł, Maździarz M, Wolak I, Harnisz M, Korzeniewska E. Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119303. [PMID: 37832303 DOI: 10.1016/j.jenvman.2023.119303] [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: 06/28/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.
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Affiliation(s)
- Magdalena Męcik
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Martyna Buta-Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Izabela Wolak
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
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14
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Chen D, Zou J, Chen D, He X, Zhang C, Li J, Lan S, Liu ZJ, Zou S, Qian X. Chicken manure application alters microbial community structure and the distribution of antibiotic-resistance genes in rhizosphere soil of Cinnamomum camphora forests. FEMS Microbiol Ecol 2023; 99:fiad155. [PMID: 38006232 PMCID: PMC10710299 DOI: 10.1093/femsec/fiad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 11/26/2023] Open
Abstract
The distribution of antibiotic-resistance genes (ARGs) in environmental soil is greatly affected by livestock and poultry manure fertilization, the application of manure will lead to antibiotic residues and ARGs pollution, and increase the risk of environmental pollution and human health. Cinnamomum camphora is an economically significant tree species in Fujian Province, China. Here, through high-throughput sequencing analysis, significant differences in the composition of the bacterial community and ARGs were observed between fertilized and unfertilized rhizosphere soil. The application of chicken manure organic fertilizer significantly increased the relative abundance and alpha diversity of the bacterial community and ARGs. The content of organic matter, soluble organic nitrogen, available phosphorus, nitrate reductase, hydroxylamine reductase, urease, acid protease, β-glucosidase, oxytetracycline, and tetracycline in the soil of C. camphora forests have significant effects on bacterial community and ARGs. Significant correlations between environmental factors, bacterial communities, and ARGs were observed in the rhizosphere soil of C. camphora forests according to Mantel tests. Overall, the findings of this study revealed that chicken manure organic fertilizer application has a significant effect on the bacterial community and ARGs in the rhizosphere soil of C. camphora forests, and several environmental factors that affect the bacterial community and ARGs were identified.
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Affiliation(s)
- Deqiang Chen
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Jiawei Zou
- School of Pharmacy, Fujian Medical University, No. 1 Xuefu North Road, University Town, Fuzhou 350002, Fujian Province, China
| | - Dexing Chen
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Xin He
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Jinwei Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Siren Lan
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Zhong-Jian Liu
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Shuangquan Zou
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Colleage of Landscape Architecture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
| | - Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, Fujian Province, China
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15
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Zhou SYD, Huang FY, Su W, Lie Z, Liu Y, Lin C, Yang K, Meng Z, Liu Z, Neilson R, Su JQ, Liu J. Distinct patterns of the soil and phyllosphere antibiotic resistome in natural forest ecosystems under an altitudinal gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165346. [PMID: 37419346 DOI: 10.1016/j.scitotenv.2023.165346] [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: 05/04/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Warming affects microbial functioning of soil and the phyllosphere across global ecosystems. However, little is known about the impact of increasing temperature on antibiotic resistome profiles in natural forests. To address this issue, we investigated antibiotic resistance genes (ARGs) in both soil and the plant phyllosphere using an experimental platform established in a forest ecosystem that delivers a temperature difference of 2.1 °C along an altitudinal gradient. Principal Coordinate Analysis (PCoA) showed that there were significant differences in the composition of soil and plant phyllosphere ARGs at different altitudes (P = 0.001). The relative abundance of phyllosphere ARGs and mobile genetic elements (MGEs) and soil MGEs increased with temperature. More resistance gene classes increased in abundance in the phyllosphere (10 classes) than soil (2 classes), and a Random Forest model analysis suggested that phyllosphere ARGs were more sensitive to temperature change than soil. Increasing temperature as a direct consequence of an altitudinal gradient, and the relative abundance of MGEs were the main drivers that shaped the profiles of ARGs in the phyllosphere and soil. Biotic and abiotic factors affected phyllosphere ARGs indirectly via MGEs. This study enhances our understanding of the influence of altitude gradients on resistance genes in natural environments.
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Affiliation(s)
- Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Wei Su
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Zhongkai University of Agriculture and Engineering, 24 Dongsha Street, Haizhu District, Guangzhou 510225, China
| | - Zhiyang Lie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Yue Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Kai Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Ze Meng
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Juxiu Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China.
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16
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Wu J, Guo S, Lin H, Li K, Li Z, Wang J, Gaze WH, Zou J. Uncovering the prevalence and drivers of antibiotic resistance genes in soils across different land-use types. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118920. [PMID: 37660639 DOI: 10.1016/j.jenvman.2023.118920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
The emergence and spread of antibiotic resistance genes (ARGs) in soil due to animal excreta and organic waste is a major threat to human health and ecosystems, and global efforts are required to tackle the issue. However, there is limited knowledge of the variation in ARG prevalence and diversity resulting from different land-use patterns and underlying driving factors in soils. This study aimed to comprehensively characterize the profile of ARGs and mobile genetic elements and their drivers in soil samples collected from 11 provinces across China, representing three different land-use types, using high-throughput quantitative polymerase chain reaction and 16S rRNA amplicon sequencing. Our results showed that agricultural soil had the highest abundance and diversity of ARGs, followed by tea plantation and forest land. A total of 124 unique ARGs were detected in all samples, with shared subtypes among different land-use patterns indicating a common origin or high transmission frequency. Moreover, significant differences in ARG distribution were observed among different geographical regions, with the greatest enrichment of ARGs found in southern China. Biotic and abiotic factors, including soil properties, climatic factors, and bacterial diversity, were identified as the primary drivers associated with ARG abundance, explaining 71.8% of total ARG variation. The findings of our study demonstrate that different land-use patterns are associated with variations in ARG abundance in soil, with agricultural practices posing the greatest risk to human health and ecosystems regarding ARGs. Our identification of biotic and abiotic drivers of ARG abundance provides valuable insights into strategies for mitigating the spread of these genes. This study emphasizes the need for coordinated and integrated approaches to address the global antimicrobial resistance crisis.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Guo
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyan Lin
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejie Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment & Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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17
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Han B, Yang F, Shen S, Mu M, Zhang K. Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165109. [PMID: 37385504 DOI: 10.1016/j.scitotenv.2023.165109] [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: 04/24/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
The changes of paddy soil habitat profoundly affect the structure and function of soil microorganisms, but how this process drives the growth and spread of manure- derived antibiotic resistance genes (ARGs) after entering the soil is unclear. Herein, this study explored the environmental fate and behavior of various ARGs in the paddy soil during rice growth period. Results showed that most ARG abundances in flooded soil was lower than that in non-flooded soil during rice growth (decreased by 33.4 %). And soil dry-wet alternation altered microbial community structure in paddy field (P < 0.05), showing that Actinobacteria and Firmicutes increased in proportion under non-flooded conditions, and Chloroflexi, Proteobacteria and Acidobacteria evolved into the dominant groups in flooded soil. Meanwhile, the correlation between ARGs and bacterial communities was stronger than that with mobile genetic elements (MGEs) in both flooded and non-flooded paddy soils. Furthermore, soil properties, especially oxidation reduction potential (ORP), were proved to be an essential factor in regulating the variability of ARGs in the whole rice growth stage by structural equation model, with a direct influence (λ = 0.38, P < 0.05), following by similar effects of bacterial communities and MGEs (λ = 0.36, P < 0.05; λ = 0.29, P < 0.05). This study demonstrated that soil dry-wet alternation effectively reduced the proliferation and dissemination of most ARGs in paddy fields, providing a novel agronomic measure for pollution control of antibiotic resistance in farmland ecosystem.
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Affiliation(s)
- Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China.
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China
| | - Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China.
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18
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Mei Z, Fu Y, Wang F, Xiang L, Hu F, Harindintwali JD, Wang M, Virta M, Hashsham SA, Jiang X, Tiedje JM. Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132388. [PMID: 37639796 DOI: 10.1016/j.jhazmat.2023.132388] [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: 05/29/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.
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Affiliation(s)
- Zhi Mei
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Yuhao Fu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Leilei Xiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Hu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyi Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Geographical Sciences, Nantong University, Nantong 226001, China
| | - Marko Virta
- Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Syed A Hashsham
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
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19
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Xu JM, Lv Y, Xu K, Liu X, Wang K, Zi HY, Zhang G, Wang AJ, Lu S, Cheng HY. Long-distance responses of ginger to soil sulfamethoxazole and chromium: Growth, co-occurrence with antibiotic resistance genes, and consumption risk. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122081. [PMID: 37414118 DOI: 10.1016/j.envpol.2023.122081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
Abstract
The coexistence of antibiotics and heavy metals in agroecosystems is nonnegligible, which permits the promotion of antibiotic resistance genes (ARGs) in crops, thus posing a potential threat to humans along the food chain. In this study, we investigated the bottom-up (rhizosphere→rhizome→root→leaf) long-distance responses and bio-enrichment characteristics of ginger to different sulfamethoxazole (SMX) and chromium (Cr) contamination patterns. The results showed that ginger root systems adapted to SMX- and/or Cr-stress by increasing humic-like exudates, which may help to maintain the rhizosphere indigenous bacterial phyla (i.e., Proteobacteria, Chloroflexi, Acidobacteria and Actinobacteria). The root activity, leaf photosynthesis and fluorescence, and antioxidant enzymes (SOD, POD, CAT) of ginger were significantly decreased under high-dose Cr and SMX co-contamination, while a "hormesis effect" was observed under single low-dose SMX contamination. For example, CS100 (co-contamination of 100 mg/L SMX and 100 mg/L Cr) caused the most severe inhibition to leaf photosynthetic function by reducing photochemical efficiency (reflected on PAR-ETR, φPSII and qP). Meanwhile, CS100 induced the highest ROS production, in which H2O2 and O2·- increased by 328.82% and 238.00% compared with CK (the blank control without contamination). Moreover, co-selective stress by Cr and SMX induced the increase of ARG bacterial hosts and bacterial phenotypes containing mobile elements, contributing to the high detected abundance of target ARGs (sul1, sul2) up to 10-2∼10-1 copies/16S rRNA in rhizomes intended for consumption.
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Affiliation(s)
- Jia-Min Xu
- School of Civil and Environmental Engineering, Harbin Institute of Technology-Shenzhen (HIT-SZ), Shenzhen, 518055, China; State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Xiaohui Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Kai Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Hu-Yi Zi
- School of Civil and Environmental Engineering, Harbin Institute of Technology-Shenzhen (HIT-SZ), Shenzhen, 518055, China; State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Guodong Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ai-Jie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology-Shenzhen (HIT-SZ), Shenzhen, 518055, China; State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Shaoyong Lu
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hao-Yi Cheng
- School of Civil and Environmental Engineering, Harbin Institute of Technology-Shenzhen (HIT-SZ), Shenzhen, 518055, China; State Key Laboratory of Urban Water Resources and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China.
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20
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Seyoum MM, Ashworth AJ, Feye KM, Ricke SC, Owens PR, Moore PA, Savin M. Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes. Front Microbiol 2023; 14:1227006. [PMID: 37886073 PMCID: PMC10598662 DOI: 10.3389/fmicb.2023.1227006] [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: 05/25/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.
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Affiliation(s)
- Mitiku Mihiret Seyoum
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J. Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Kristina M. Feye
- Cellular and Molecular Biology, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Phillip R. Owens
- USDA-ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Philip A. Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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21
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Wu J, Guo S, Li K, Li Z, Xu P, Jones DL, Wang J, Zou J. Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties. CHEMOSPHERE 2023; 336:139272. [PMID: 37343633 DOI: 10.1016/j.chemosphere.2023.139272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Guo
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejie Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pinshang Xu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, 6105, Australia
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
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22
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Zhang S, Li T, Hu J, Li K, Liu D, Li H, Wang F, Chen D, Zhang Z, Fan Q, Cui X, Che R. Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118037. [PMID: 37178462 DOI: 10.1016/j.jenvman.2023.118037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of "grain for green" project on soil health.
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Affiliation(s)
- Song Zhang
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China; State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Ting Li
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinming Hu
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Kexin Li
- Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Dong Liu
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Haixia Li
- Faculty of Land Resource Engineering, Kunming University of Science and Technology, Kunming, 650093, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danhong Chen
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Zejin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuping Fan
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China.
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23
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Nie C, Hou Y, Liu F, Dong Q, Li Z, Han P, Tong M. Efficient peroxymonosulfate activation by magnetic MoS 2@Fe 3O 4 for rapid degradation of free DNA bases and antibiotic resistance genes. WATER RESEARCH 2023; 239:120026. [PMID: 37182307 DOI: 10.1016/j.watres.2023.120026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/16/2023]
Abstract
Antibiotic resistance genes (ARGs) have become as emerging contaminant with great concerns worldwide due to their threats to human health. It is thus urgent to develop techniques to degrade ARGs in water. In this study, MoS2@Fe3O4 (MF) particles were fabricated and used to activate peroxymonosulfate (PMS) for the degradation of four types of free DNA bases (T, A, C, and G, major components of ARGs) and ARGs. We found that MF/PMS system could effectively degrade all four DNA bases (T within 10 min, A within 30 min, C within 5 min, and G within 5 min) in very short time. During the reaction process, MF could activate PMS to form the reactive radicals such as ·OH, SO4·-, O2·-, and 1O2, contributing to the degradation of DNA bases. Due to the low adsorption energy, high charge transfer, and great capability for PMS cleavage, MF exhibited excellent PMS adsorption and activation performances. MoS2 in MF could enhance the cycle of Fe(III)/Fe(II), improving the catalytic performance. Excellent catalytic performances of MF/PMS system were achieved in complex water matrix (including different solution pH, coexisting of anions and natural organic matter) as well as in real water samples (including tap water, river water, sea water, and sewage) especially under high salinity conditions due to the generation of Cl· radicals and HClO species. MF/PMS system could also efficiently degrade ARGs (chromosomal kanR and plasmid gmrA) and DNA extracted from antibiotic resistant bacteria (ARB) in super-short time. Moreover, complete disinfection of two types of model ARB (E. coli K-12 MG 1655 and E. coli S17-1) could also be achieved in MF/PMS system. The high degradation performances of MF/PMS system achieved in the reused experiments and the 14-day continuous flow reactor experiments indicated the stability of MF particles. Due to the magnetic property, it would be convenient to separate MF particles from water after use via using magnet, facilitating their reuse of MF and avoiding potential water contamination by catalysts. Overall, this study not only provided a deep insight on Fe/Mo-triggered PMS activation process, but also provided an effective and reliable approach for the treatment of DNA bases, ARGs, DNA, and ARB in water.
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Affiliation(s)
- Chenyi Nie
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Yanghui Hou
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Fuyang Liu
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Qiqi Dong
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Zhengmao Li
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China
| | - Peng Han
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China.
| | - Meiping Tong
- The Key Laboratory of Water and Sediment Sciences, Ministry of Education, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, PR China.
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24
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Liu Y, Feng M, Johansen A, Cheng D, Xue J, Feng Y, Fan S, Li Z. Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161785. [PMID: 36736399 DOI: 10.1016/j.scitotenv.2023.161785] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.
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Affiliation(s)
- Yuanwang Liu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Minmin Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Anders Johansen
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, Roskilde 4000, Denmark
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Scion, Private Bag 29237, Christchurch 8440, New Zealand
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuanghu Fan
- College of Life Science, Langfang Normal University, Langfang 065000, China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Zhang MS, Liang SZ, Zhang WG, Chang YJ, Lei Z, Li W, Zhang GL, Gao Y. Field ponding water exacerbates the dissemination of manure-derived antibiotic resistance genes from paddy soil to surrounding waterbodies. Front Microbiol 2023; 14:1135278. [PMID: 37007487 PMCID: PMC10065064 DOI: 10.3389/fmicb.2023.1135278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
Farmlands fertilized with livestock manure-derived amendments have become a hot topic in the dissemination of antibiotic resistance genes (ARGs). Field ponding water connects rice paddies with surrounding water bodies, such as reservoirs, rivers, and lakes. However, there is a knowledge gap in understanding whether and how manure-borne ARGs can be transferred from paddy soil into field ponding water. Our studies suggest that the manure-derived ARGs aadA1, bla1, catA1, cmlA1-01, cmx(A), ermB, mepA and tetPB-01 can easily be transferred into field ponding water from paddy soil. The bacterial phyla Crenarchaeota, Verrucomicrobia, Cyanobacteria, Choloroflexi, Acidobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are potential hosts of ARGs. Opportunistic pathogens detected in both paddy soil and field ponding water showed robust correlations with ARGs. Network co-occurrence analysis showed that mobile genetic elements (MGEs) were strongly correlated with ARGs. Our findings highlight that manure-borne ARGs and antibiotic-resistant bacteria in paddy fields can conveniently disseminate to the surrounding waterbodies through field ponding water, posing a threat to public health. This study provides a new perspective for comprehensively assessing the risk posed by ARGs in paddy ecosystems.
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Affiliation(s)
- Ming-Sha Zhang
- School of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Si-Zhou Liang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Wei-Guo Zhang
- School of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, China
- *Correspondence: Wei-Guo Zhang, ; Ya-Jun Chang,
| | - Ya-Jun Chang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing, China
- *Correspondence: Wei-Guo Zhang, ; Ya-Jun Chang,
| | - Zhongfang Lei
- School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Wen Li
- School of Life Sciences, Nanjing University, Nanjing, China
| | | | - Yan Gao
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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26
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Cao H, Jiao Q, Cheng L, Song L, Xun M, Yang H. Occurrence and prevalence of antibiotic resistance genes in apple orchard after continual application of anaerobic fermentation residues of pig manure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:29229-29242. [PMID: 36409412 DOI: 10.1007/s11356-022-24320-x] [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: 08/09/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Fermented organic fertilizers made from pig manure contaminated with antibiotics are widely used in fruit tree production. However, their effects on the residual antibiotics and the spread of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in apple orchards are still largely unknown. In the present study, we detected 100 ARGs and 10 MGEs that were transferred from pig manure to an apple orchard. Compared with the original pig manure, significantly greater concentrations of tetracycline, chlortetracycline, oxytetracycline, sulfadiazine, and salfamethyldiazine were observed in anaerobic fermentation residues of the pig manure. The total relative abundance levels of ARGs on the apple pericarp surface, in the orchard soil treated with biogas slurry, and in the orchard soil treated with biogas residue were 122.5, 5.2, 1.4 times higher than those in pristine soil, respectively, which were primarily attributed to the increase in the relative abundance of some ARG subtypes, including blaCTX-M, blaTEM, ermC, sul2, tetO, vgaB, and vgb. Long-term biogas slurry and biogas residue applications to orchard soil enriched bioaccumulation of 10 ARGs and 1 MGEs on the apple pericarp surface with 67.98 the highest factor. This research indicates that the application of anaerobic fermentation residues of pig manure promoted the spread of ARGs in the soil and fruits and increased the level of ARG pollution in the orchard. Results of this study highlight the importance of assessing the ecological safety of organic fertilizers from the perspective of ARGs and indicate that efforts should be devoted to further reducing ARG levels in pig manure before its application to farmland.
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Affiliation(s)
- Hui Cao
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, Shandong Province, China
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Qian Jiao
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, Shandong Province, China
| | - Liangmei Cheng
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, Shandong Province, China
| | - Linhui Song
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, Shandong Province, China
| | - Mi Xun
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Hongqiang Yang
- College of Horticulture Science and Engineering, State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China.
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Li Z, Shen J, Wang F, Wang M, Shen J, Li Y, Zhu Q, Wu J. Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields. Front Microbiol 2023; 13:1075234. [PMID: 36762093 PMCID: PMC9904388 DOI: 10.3389/fmicb.2022.1075234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/29/2022] [Indexed: 01/26/2023] Open
Abstract
The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.
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Affiliation(s)
- Zongming Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China
| | - Jupei Shen
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Fangfang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Meihui Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China
| | - Jianlin Shen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China,*Correspondence: Jianlin Shen,
| | - Yong Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China
| | - Jinshui Wu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China,College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, China
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28
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Xu F, Sun G, Du W, Ai F, Yin Y, Guo H. Impacts of Chemical and Organic Fertilizers on the Bacterial Communities, Sulfonamides and Sulfonamide Resistance Genes in Paddy Soil Under Rice-Wheat Rotation. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 110:20. [PMID: 36547725 DOI: 10.1007/s00128-022-03642-z] [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: 04/07/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
The responses of sulfonamides, sulfonamide-resistance genes (sul) and soil bacterial communities to different fertilization regimes were investigated by performing a field experiment using paddy soil with no fertilizer applied, chemical fertilizer applied, organic fertilizer applied, and combination of chemical and organic fertilizer applied. Applying organic fertilizer increased the bacterial community diversity and affected the bacterial community composition. Eutrophic bacteria (Bacteroidetes, Gemmatimonadetes, and Proteobacteria) were significantly enriched by applying organic fertilizer. It was also found organic fertilizer application increased sulfamethazine content and the relative abundances of sul1 and sul2 in the soil. In contrast, applying chemical fertilizer significantly increased the abundance of Nitrospirae, Parcubacteria, and Verrucomicrobia and caused no obvious changes on sul. Correlation analysis indicated that sul enrichment was associated with the increases in sulfamethazine content and potential hosts (e.g., Novosphingobium and Rhodoplanes) population. The potential ecological risks of antibiotics in paddy soil with organic fertilizer applied cannot be ignored.
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Affiliation(s)
- Fen Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, 210046, Nanjing, China
| | - Guofeng Sun
- Key Laboratory for Crop and Animal Integrated Farming, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environments, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, China
| | - Wenchao Du
- School of Environment, Nanjing Normal University, 210036, Nanjing, China
| | - Fuxun Ai
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, 210046, Nanjing, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, 210046, Nanjing, China
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, 210046, Nanjing, China.
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29
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Peng S, Song D, Zhou B, Hua Q, Lin X, Wang Y. Persistence of Salmonella Typhimurium and antibiotic resistance genes in different types of soil influenced by flooding and soil properties. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 248:114330. [PMID: 36436254 DOI: 10.1016/j.ecoenv.2022.114330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/30/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Salmonella is a zoonotic foodborne bacterial pathogen that can seriously harm health. Persistence of Salmonella and antibiotic resistance genes (ARGs) in different types of soil under flooding and natural conditions are rare explored. This study investigated the dynamic changes of the Salmonella, ARGs and bacterial communities in three types of soils applied with pig manure in lab scale. Abundance of the Salmonella Typhimurium in soils reduced to the detection limit varied from 40 to 180 days, most of the Salmonella did not survive in soil for more than 90 days. Flooding and soil texture (content of sand) promote the decline rate of Salmonella. No Salmonella was found have acquired resistance gene from the soil or manure after 90 days. 64 ARGs and 11 MGEs were quantified, abundance of these genes and risky ARGs both gradually decline along with the extension of time. Most of the extrinsic ARGs cannot colonize in soil, cellular protection and antibiotic deactivation were their main resistance mechanism. Multidrug resistance and efflux pump were the dominant class and mechanism of soil intrinsic ARGs. Flooding can affect the ARGs profiles by reducing the types of extrinsic ARGs invaded into soil and inhibit the proliferation of intrinsic genes. Soil sand content, soil moisture and nutrition concentrations had significant direct effect on the abundance or profile of ARGs. Soil bacterial community structures also changed along with the extension of time and affected by flooding. Network analyses between ARGs and bacteria taxa revealed that Actinobacteria and Myxococcia were the main hosts of intrinsic ARGs, some taxa may play a role in inhibiting extrinsic ARGs colonization in the soils. These findings unveil that saturate soil with water may play a positive role in reducing potential risk of Salmonella and ARGs in the farmland environment.
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Affiliation(s)
- Shuang Peng
- College of Environment and Ecology, Jiangsu Open University, Nanjing, Jiangsu 210017, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, Jiangsu 210095, PR China
| | - Dan Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China
| | - Beibei Zhou
- College of Environment and Ecology, Jiangsu Open University, Nanjing, Jiangsu 210017, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China
| | - Qingqing Hua
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, PR China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, Jiangsu 210095, PR China.
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30
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Liao H, Li H, Duan CS, Zhou XY, An XL, Zhu YG, Su JQ. Metagenomic and viromic analysis reveal the anthropogenic impacts on the plasmid and phage borne transferable resistome in soil. ENVIRONMENT INTERNATIONAL 2022; 170:107595. [PMID: 36283158 DOI: 10.1016/j.envint.2022.107595] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Anthropogenic land use changes have been recognized with significant effects on the abundance and diversity of antibiotic resistance genes (ARGs) in soil, but their impacts on ARGs with potential health risk remained poorly understood. In this study, paired metagenomes and viromes were obtained from soils (Anthrosols and Nitisols) with different land uses including urban parks, road verge, forests, vegetable and paddy in a subtropical city, Xiamen, and soils (Anthrosols) with various long-term fertilization treatments in Dezhou located in temperate region, respectively, to explore the influence of anthropogenic activity on soil resistome. The diversity and abundance of antibiotic resistance genes (ARGs) were profiled, and the risk associated factors of ARGs, i.e., genetic location, host, and co-existence with virulence factors (VFs), were systematically investigated at reads and contigs level. We observed that agricultural areas significantly enriched human-related ARGs and viruses, and positively related with clinical ARGs. Most of the ARG-carrying contigs were chromosomes (∼85 %), while, human-related ARGs presented a higher odds ratio to locate on plasmids. Soil VFs exhibited land use pattern and distinct distribution between chromosome and plasmids, but less mobile than ARGs. Analysis of 131,014 soil viral genomes indicated that they barely encoded ARGs, nevertheless, transduction of VLPs was implicated in the spread of ARGs. The results can be mutually verified in Xiamen and Dezhou datasets. Overall, the agricultural soils with dry-farming are hotspots for the clinical ARGs, and the transmission of clinical ARGs between human dominated environments and soil is primarily mediated by plasmids, rather than bacterial chromosomes, and the transduction of human-gut related viruses could participate the process. These results highlight the importance of tracking the fate of clinical ARGs for better evaluating the impacts of human activities on soil resistome.
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Affiliation(s)
- Hu Liao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen-Song Duan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Lin D, Huang D, Zhang J, Yao Y, Zhang G, Ju F, Xu B, Wang M. Reduction of antibiotic resistance genes (ARGs) in swine manure-fertilized soil via fermentation broth from fruit and vegetable waste. ENVIRONMENTAL RESEARCH 2022; 214:113835. [PMID: 35810807 DOI: 10.1016/j.envres.2022.113835] [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: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The issue of growing increase of antibiotic resistance genes (ARGs) in manure-fertilized soil needs urgently addressing. In this study, fermentation broth from fruit and vegetable waste was prepared to reduce ARG abundance in swine manure-fertilized soils. With a six-month field experiment, we found that swine manure-fertilized soil had significantly higher ARG abundance than soil applied with chemical fertilizer. As expected, the homemade fermentation broth significantly reduced ARG abundance in swine manure-fertilized soil, possibly through the decrease of abundance of Actinomyces, in which there was a 48.0%, 51.9%, and 66.7% decrease in the abundance of Nocardioides, Streptomyces, and Nonomuraea, respectively. With the bacteriostatic experiment, we observed that fermentation broth (5 mL/L) significantly inhibited the growth and metabolism in Actinomycetes spp. and Nocardioides sp., in terms of ATPase and PDH activity. These findings confirmed that the inhibition of Actinobacteria, some of the most dominant ARG hosts, was one of the main mechanisms responsible for the decrease in ARG abundance in fermentation broth-treated soil. This study provides field-scale evidence of a feasible strategy for controlling farmland ARG pollution, which is of utmost importance for soil health in the context of sustainable agriculture.
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Affiliation(s)
- Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Dan Huang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yanlai Yao
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Baile Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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Wang C, Jia Y, Wang Q, Yan F, Wu M, Li X, Fang W, Xu F, Liu H, Qiu Z. Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China. ENVIRONMENTAL RESEARCH 2022; 214:113748. [PMID: 35750128 DOI: 10.1016/j.envres.2022.113748] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 05/27/2023]
Abstract
In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.
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Affiliation(s)
- Can Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China; State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil&Water Pollution, PR China
| | - Yinxue Jia
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Qiqi Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Fangfang Yan
- Panzhihua City Company, Sichuan Tobacco Company, China National Tobacco Corporation, Panzhihua, 617000, Sichuan, PR China
| | - Minghui Wu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Xing Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Weizhen Fang
- Analysis & Testing Center, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China
| | - Fei Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China
| | - Huakang Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China.
| | - Zhongping Qiu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, PR China.
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33
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Yang Y, Li T, Liu P, Li H, Hu F. The formation of specific bacterial communities contributes to the enrichment of antibiotic resistance genes in the soil plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129247. [PMID: 35739766 DOI: 10.1016/j.jhazmat.2022.129247] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.
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Affiliation(s)
- Yang Yang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Teng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu 210023, China
| | - Huixin Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Liu W, Cheng Y, Guo J, Duan Y, Wang S, Xu Q, Liu M, Xue C, Guo S, Shen Q, Ling N. Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129163. [PMID: 35739703 DOI: 10.1016/j.jhazmat.2022.129163] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/21/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs).
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Affiliation(s)
- Wenbo Liu
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science & Technology, Hangzhou 310023, Zhejiang, China
| | - Yanfen Cheng
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Junjie Guo
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China; Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yinghua Duan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuang Wang
- Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin 150080, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Manqiang Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Ning Ling
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, Gansu, China; Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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35
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Qing L, Qigen D, Jian H, Hongjun W, Jingdu C. Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119368. [PMID: 35489540 DOI: 10.1016/j.envpol.2022.119368] [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: 10/07/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils.
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Affiliation(s)
- Li Qing
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Dai Qigen
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Hu Jian
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Wu Hongjun
- Yangzhou Supervision & Inspection Center for Agri-products, Yangzhou, 225101, China
| | - Chen Jingdu
- Yangzhou Municipal Bureau of Agriculture and Rural Affairs, Yangzhou, 225000, China
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36
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Bech TB, Badawi N, Rosenbom AE. Impact of surface-applied liquid manure on the drainage resistance profile of an agricultural tile-drained clay till field. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:656-669. [PMID: 35435263 DOI: 10.1002/jeq2.20354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Dissemination of antibiotic resistance genes (ARGs) in aquatic environments is a concern due to human and animal health. Application of liquid manure on agricultural land is an important source of ARGs, where pathogens, antibiotic-resistant bacteria, and selective agents are released. To improve our understanding of ARGs spreading through soils, our main objective was to evaluate the effectiveness of the soil as a barrier protecting water resources. Over the course of a year, profiles and abundances of ARGs and mobile genetic elements in soil and drainage from an agricultural tile-drained clay till field were investigated upon liquid pig manure application by applying high-throughput quantitative polymerase chain reaction targeting 143 genes. The findings were as follows: (a) 97 genes were detected, where only the transposon gene tnpA-03/ IS6 was shared between the genes detected in drainage and those in acidified liquid manure or fertilized soils, indicating that liquid manure application had a limited impact on the drainage resistance profile; (b) intI1 gene was present in ∼60% of drainage samples in concentrations up to 1,634 intI1 ml-1 ; and (c) evapotranspiration from barley (Hordeum vulgare L., 'KWS Irina') and a low groundwater table appeared to reduce preferential transport to drainage during the first 3 mo of liquid manure application. Interestingly, the first preferential transport to drainage was observed immediately after the harvest of spring barley. Overall, during the monitoring year we found the soil to be an effective barrier against the spread of fecal ARGs even though the occurrence of the intI1 gene questions the barrier effect from previous years.
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Affiliation(s)
- Tina B Bech
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Nora Badawi
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Annette E Rosenbom
- Dep. of Geochemistry, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
- Rambøll Danmark A/S, Hannemanns Allé 53, 2300 Copenhagen S, Copenhagen, Denmark
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37
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Meng M, Li Y, Yao H. Plasmid-Mediated Transfer of Antibiotic Resistance Genes in Soil. Antibiotics (Basel) 2022; 11:antibiotics11040525. [PMID: 35453275 PMCID: PMC9024699 DOI: 10.3390/antibiotics11040525] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 12/18/2022] Open
Abstract
Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.
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Affiliation(s)
- Miaoling Meng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- Correspondence: ; Tel.: +86-0574-8678-4812
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38
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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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Fu Y, Wang F, Wang Z, Mei Z, Jiang X, Schäffer A, Virta M, Tiedje JM. Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:151386. [PMID: 34742956 DOI: 10.1016/j.scitotenv.2021.151386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.
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Affiliation(s)
- Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andreas Schäffer
- RWTH Aachen University, Institute for Environmental Research, Aachen 52074, Germany
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
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40
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Liu Y, Neal AL, Zhang X, Fan H, Liu H, Li Z. Cropping system exerts stronger influence on antibiotic resistance gene assemblages in greenhouse soils than reclaimed wastewater irrigation. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:128046. [PMID: 34986574 DOI: 10.1016/j.jhazmat.2021.128046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The effects of reclaimed wastewater (RW) irrigation on the spread of antibiotic resistance genes (ARGs) in soil is modulated by a myriad of biotic and abiotic factors and their relative significance remains vague. We compared microbial communities, assemblages of genes associated with microbial resistance to antibiotics, biocides and metals, and insertion sequences (ISs) in soils following 16 years of irrigation with groundwater (GW), RW or alternately with GW and RW in two greenhouses with different cropping systems, using shotgun metagenome sequencing. The results showed that cropping system exerted greater influence than irrigation on the profile of ISs and resistance genes. This influence was most strongly associated with concentrations of copper, mercury and perfloxacin in the soils. There was no significant difference in soil ARG profiles between continuous RW irrigation and alternating GW and RW irrigation. Proteobacteria, Actinobacteria and Firmicutes and a limited number of ISs were closely associated with the detected ARGs. Most ARGs were found to co-occur with metal and biocide resistance genes through the mechanism of efflux pumps. These findings highlight the significance of understanding and improving crop management in mitigating the dissemination of ARGs in soils irrigated with RW.
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Affiliation(s)
- Yuan Liu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Devon EX22 2SB, UK
| | - Xiaoxian Zhang
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Haiyan Fan
- Beijing Engineering Research Center for Non-conventional Water Resources Utilization and Water Saving, Beijing Water Science and Technology Institute, Beijing 100048, China
| | - Honglu Liu
- Beijing Engineering Research Center for Non-conventional Water Resources Utilization and Water Saving, Beijing Water Science and Technology Institute, Beijing 100048, China
| | - Zhongyang Li
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
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Liu Y, Cheng D, Xue J, Feng Y, Wakelin SA, Weaver L, Shehata E, Li Z. Fate of bacterial community, antibiotic resistance genes and gentamicin residues in soil after three-year amendment using gentamicin fermentation waste. CHEMOSPHERE 2022; 291:132734. [PMID: 34743798 DOI: 10.1016/j.chemosphere.2021.132734] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 05/20/2023]
Abstract
Over a three-year field trial, the impacts of composted and raw gentamicin fermentation waste (GFW) application to land on residual soil gentamicin levels, physicochemical properties, bacterial community composition, and antibiotic resistance genes (ARGs) were assessed. In the saline-alkali soil tested, GFW application decreased electrical conductivity (EC) and pH. Importantly, there was no measurable long-term accumulation of gentamicin as a result of GFW addition. Changes in the abundance of Bacillus was primarily associated with degradation of gentamicin in soil, whereas wider (i.e. more general) shifts in bacterial communities over the treatments was linked to alteration of soil physicochemical properties, particularly pH, total nitrogen, dissolved organic carbon, EC, NO3--N and NH4+-N. Compared with other treatments, soils receiving composted GFW harbored more types of ARGs and significantly higher (P < 0.05) abundances of mobile genes elements (MGEs) (especially IncQ and Int1) and aminoglycoside ARGs (especially aminoglycoside phosphotransferases genes, APH). Finally, the abundances of ARGs in soils receiving raw and composted GFW were 59.60% and 50.26% higher than that in soils only receiving chemical fertilizer, respectively. Specifically, the abundances of APH, especially strB, were significantly higher than other kinds of ARGs (P < 0.05). The results of linear regression and partial least squares path model showed that MGEs, including plasmids, integrons, and transposons, along with soil properties (EC and NH4+-N) were the main factors associated with change in ARGs. Furthermore, different MGEs were involved in different transfer mechanisms of specific ARGs. Our findings demonstrated the potential risks of using raw and composted GFW as fertilizer, and suggest potential solutions to this problem.
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Affiliation(s)
- Yuanwang Liu
- Hebei Key Laboratory of Applied Chemistry, Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, 066004, PR China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; Scion, Private Bag, 29237, Christchurch, New Zealand
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | | | - Louise Weaver
- Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand
| | - Ebrahim Shehata
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; Institute of Animal science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China.
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42
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Cui E, Fan X, Hu C, Neal AL, Cui B, Liu C, Gao F. Reduction effect of individual N, P, K fertilization on antibiotic resistance genes in reclaimed water irrigated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113185. [PMID: 35030524 DOI: 10.1016/j.ecoenv.2022.113185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) in soil under reclaimed water irrigation poses a potential environmental risk. Regulation of NPK fertilizer could influence the behavior of bacterial communities, mobile genetic elements (MGEs), and soil properties, which determine the fate of ARGs. To identify the key element in NPK fertilizer and realize efficient regulation, we explored the effect of individual N, P, K fertilization on ARG variation in tomato rhizosphere and bulk soils. Compared with an unfertilized treatment, N fertilization resulted in greater decreases in the abundance of ARGs (decreases of 24.06%-73.09%) than did either P fertilization (increases of up to 35.84%, decreases of up to 58.80%) or K fertilization (decreases of 13.47%-72.47%). The influence of different forms of N (CO(NH2)2, NaNO3, and NH4HCO3), P (Ca(H2PO4)2 and CaMgO4P+), and K (KCl and K2(SO4)) fertilizers was also investigated in this study, and showed the influence of NaNO3, CaMgO4P+, and K2(SO4) on reducing ARGs abundance was greater in different types of N, P, K fertilizers. Bacterial communities showed the strongest response to N fertilization. The reduced bacterial diversity and abundance of ARG-host and non-host organisms explained the decline of total ARG abundance in soil. In soils fertilized with either P or K, the effect of soil properties, especially total nitrogen and pH, on ARG variation was greater than that of bacterial community and MGEs. These results suggest that N regulation of in NPK fertilizer may be an effective way to reduce the risks of ARGs in soil associated with reclaimed water irrigation.
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Affiliation(s)
- Erping Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chao Hu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Devon EX20 2SB, UK
| | - Bingjian Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chuncheng Liu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Feng Gao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
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Wang X, Han C, Lan B, Wang C, Zhu G. Antibiotic resistance genes on the Qinghai-Tibet Plateau above an elevation of 5,000 m. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:4508-4518. [PMID: 34414535 DOI: 10.1007/s11356-021-16007-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance genes (ARGs) widely occur in both anthropogenic and remote environments. Several studies have investigated the distribution of antibiotic resistance in natural environments. However, the occurrence and diversity of ARGs in remote environments at high elevations have not yet been well elucidated. Abundance, diversity, as well as influencing factors of ARGs in different ecosystems on the Qinghai-Tibet Plateau beyond elevation 5,000 m were explored, using high-throughput quantitative PCR. Totally, 197 ARGs and 12 mobile genetic elements (MGEs) were determined with abundances ranging from 3.75 × 106 to 2.39 × 107 and from 2.21 × 104 to 1.62 × 106 copies g-1, respectively. Both the absolute and relative abundances of ARGs in farmland were lower than those in wetland and grassland. The diversity and dominant resistance mechanism of ARG profiles showed obvious differences among these ecosystems. Bacterial communities and MGEs significantly correlated with ARG profiles, while physico-chemical factors showed little impact. The high abundance and strong positive correlation between integron intI-1 and ARGs suggested a high potential horizontal ARG transfer. Based on the results, the Qinghai-Tibet Plateau can be regarded as a considerable ARG gene pool. This study provides insights into the provenance of ARGs at high elevations.
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Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chang Han
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bangrui Lan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- South China Sea Institution, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Fu Y, Jia M, Wang F, Wang Z, Mei Z, Bian Y, Jiang X, Virta M, Tiedje JM. Strategy for Mitigating Antibiotic Resistance by Biochar and Hyperaccumulators in Cadmium and Oxytetracycline Co-contaminated Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16369-16378. [PMID: 34695355 DOI: 10.1021/acs.est.1c03434] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global prevalence of antibiotic resistance genes (ARGs) is of increasing concern as a serious threat to ecological security and human health. Irrigation with sewage and farmland application of manure or biosolids in agricultural practices introduce substantial selective agents such as antibiotics and toxic metals, aggravating the transfer of ARGs from the soil environment to humans via the food chain. To address this issue, a hyperaccumulator (Sedum plumbizincicola) combined with biochar amendment was first used to investigate the mitigation of the prevalence of ARGs in cadmium and oxytetracycline co-contaminated soil by conducting a pot experiment. The addition of biochar affected the distribution of ARGs in soil and plants differently by enhancing their prevalence in the soil but restraining transmission from the soil to S. plumbizincicola. The planting of S. plumbizincicola resulted in an increase in ARGs in the soil environment. A structural equation model illustrated that mobile genetic elements played a dominant role in shaping the profile of ARGs. Taken together, these findings provide a practical understanding for mitigating the prevalence of ARGs in this soil system with complex contamination and can have profound significance for agricultural management in regard to ARG dissemination control.
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Affiliation(s)
- Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyun Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210008, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
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45
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Mei Z, Xiang L, Wang F, Xu M, Fu Y, Wang Z, Hashsham SA, Jiang X, Tiedje JM. Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment. ENVIRONMENT INTERNATIONAL 2021; 157:106830. [PMID: 34418848 DOI: 10.1016/j.envint.2021.106830] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 05/23/2023]
Abstract
The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 104 and 1.1 × 106 in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 107 and 3.2 × 107 of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.
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Affiliation(s)
- Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leilei Xiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
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46
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Zhao Y, Hu HW, Su JQ, Hao X, Guo H, Liu YR, Zhu YG. Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13913-13922. [PMID: 34613706 DOI: 10.1021/acs.est.1c04030] [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] [Indexed: 06/13/2023]
Abstract
Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.
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Affiliation(s)
- Yi Zhao
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Xiuli Hao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaming Guo
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
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47
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Fan H, Wu S, Dong W, Li X, Dong Y, Wang S, Zhu YG, Zhuang X. Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H 218O-based DNA-Stable isotope probing and metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126440. [PMID: 34280721 DOI: 10.1016/j.jhazmat.2021.126440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 05/12/2023]
Abstract
The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.
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Affiliation(s)
- Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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48
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Qiao L, Liu X, Zhang S, Zhang L, Li X, Hu X, Zhao Q, Wang Q, Yu C. Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146502. [PMID: 34030239 DOI: 10.1016/j.scitotenv.2021.146502] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 05/26/2023]
Abstract
Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.
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Affiliation(s)
- Longkai Qiao
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Xiaoxia Liu
- Beijing Station of Agro-Environmental Monitoring, Test and Supervision Center of Agro-Environmental Quality, MOA, 100032 Beijing, China
| | - Shuo Zhang
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Luying Zhang
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Xianhong Li
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Xuesong Hu
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Qiancheng Zhao
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Qingyu Wang
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China
| | - Caihong Yu
- School of Chemistry and Environment Engineering, China University of Mining and Technology, Beijing, 100083, Beijing, China.
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49
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Luan X, Han Z, Shen Y, Yang M, Zhang Y. Assessing the effect of treated erythromycin fermentation residue on antibiotic resistome in soybean planting soil: In situ field study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146329. [PMID: 34030225 DOI: 10.1016/j.scitotenv.2021.146329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
As a by-product in the pharmaceutical industry, antibiotic fermentation residue is expected to be able to be utilized after effectively removing the antibiotics. However, evaluation of the effect of fermentation residue application on soil, especially the in situ environmental consequences considering not only the antibiotic resistance gene (ARG) abundance but also the resistome risk, has still not been sufficiently evaluated. Herein, the impact of treated erythromycin fermentation residue (EFR) on the resistome and risk score in soybean planting soil was investigated. Treated EFR application with dosages of 3750 kg (EFR250) and 7500 kg (EFR500) per hm2 soil did not increase the diversity (Shannon index, 2.84-3.38) or relative abundance (0.086-0.142 copies/16S rRNA gene) of the soil resistome compared with the Control (CK: 2.92-3.2, 0.088-0.096 copies/16S rRNA gene). Soil resistome risk scores calculated by metagenomic assembly, showing the dissemination potential of ARGs, ranged from 22.9 to 25.0, and were also not significantly different between treated EFR amended soil and the Control. Notably, the diversity of the resistome increased at the sprout stage (Mann-Whitney U test, P < 0.05) and the abundance of some ARG types (macrolide-lincosamide-streptogramin, aminoglycoside and tetracycline, etc.) shifted along the course of soybean growth (Kruskal-Wallis test, P < 0.05). Structural equation model analysis showed that the soybean growth period affected the composition of ARGs by affecting the microbial community, which was further supported by Procrustes analysis (P < 0.05) and metagenomic binning. Our findings emphasized that soil ARG abundance and resistome risk did not increase during one-time field application of treated EFR at the studied dosage. Comprehensive consideration including resistome risk and multiple influencing factors also should be given for further assessment of fermentation residue application.
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Affiliation(s)
- Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunpeng Shen
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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50
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Liao H, Bai Y, Liu C, Wen C, Yang Q, Chen Z, Banerjee S, Zhou S, Friman VP. Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage. Environ Microbiol 2021; 23:7483-7496. [PMID: 34259375 DOI: 10.1111/1462-2920.15672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 11/27/2022]
Abstract
Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.
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Affiliation(s)
- Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yudan Bai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chang Wen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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