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Mu M, Yang F, Han B, Tian G, Zhang K. Vermicompost: In situ retardant of antibiotic resistome accumulation in cropland soils. J Environ Sci (China) 2024; 141:277-286. [PMID: 38408828 DOI: 10.1016/j.jes.2023.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 02/28/2024]
Abstract
The dissemination of antibiotic resistance genes (ARGs) in soil has become a global environmental issue. Vermicomposting is gaining prominence in agricultural practices as a soil amendment to improve soil quality. However, its impact on soil ARGs remains unclear when it occurs in farmland. We comprehensively explored the evolution and fate of ARGs and their hosts in the field soil profiles under vermicompost application for more than 3 years. Vermicompost application increased several ARG loads in soil environment but decreased the high-risk bla-ARGs (blaampC, blaNDM, and blaGES-1) by log(0.04 - 0.43). ARGs in soil amended with vermicompost primarily occurred in topsoil (approximately 1.04-fold of unfertilized soil), but it is worth noting that their levels in the 40-60 cm soil layer were the same or even less than in the unfertilized soil. The microbial community structure changed in soil profiles after vermicompost application. Vermicompost application altered the microbial community structure in soil profiles, showing that the dominant bacteria (i.e., Proteobacteria, Actinobacteriota, Firmicutes) were decreased 2.62%-5.48% with the increase of soil depth. A network analysis further revealed that most of ARG dominant host bacteria did not migrate from surface soil to deep soil. In particular, those host bacteria harboring high-risk bla-ARGs were primarily concentrated in the surface soil. This study highlights a lower risk of the propagation of ARGs caused by vermicompost application and provides a novel approach to reduce and relieve the dissemination of ARGs derived from animals in agricultural production.
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Affiliation(s)
- Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Guisheng Tian
- Wuxue City Agriculture and Rural Bureau, Wuhan 435400, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; Key Laboratory of Low-carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs P. R. China, Beijing 10083, China.
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Shrivas VL, Choudhary AK, Hariprasad P, Sharma S. Transmission of antibiotic resistance through organic amendments in arable land: A 3-year field study with pigeonpea-wheat cropping system. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134378. [PMID: 38691926 DOI: 10.1016/j.jhazmat.2024.134378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
The worldwide emergence of antimicrobial resistance (AMR) poses a substantial risk to human health and environmental stability. In agriculture, organic amendments (derived from organic sources such as manure, and plant residues) are beneficial in restoring soil properties and providing essential nutrients to crops but raise concerns about harboring antibiotic resistance, which emphasizes the need for vigilant monitoring and strategic interventions in their application. The current study assessed the impact of farming practices (organic and conventional) in a three-year field experiment with pigeonpea-wheat cropping system, focusing on the transmission of AMR using culture-dependent and -independent approaches, and soil nutrient content. Markers for antibiotic resistance genes (ARGs) (aminoglycoside-aacA, β-lactam-blaTEM, chloramphenicol-cmlA1, macrolide-ermB, sulfonamides-sul1, sul2, and tetracycline-tetO) and integrons (intl1 and intl2) were targeted using qPCR. Manure amendments, particularly FYM1, exhibited a higher abundance of copies of ARGs compared to the rhizospheric soil. Organic farming was associated with higher copies of intl2, sul1, blaTEM, and tetO genes, while conventional farming showed increased copies of sul2 and ermB genes in the rhizosphere. Significant positive correlations were observed among soil nutrient contents, ARGs, and MGEs. The notable prevalence of ARGs linked to manure amendments serves as a cautionary note, demanding responsible management practices.
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Affiliation(s)
- Vijay Laxmi Shrivas
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India; Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Anil K Choudhary
- Division of Agronomy, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - P Hariprasad
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
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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: 0] [Impact Index Per Article: 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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Zheng S, Han B, Wang Y, Ding Y, Zhao R, Yang F. Occurrence and dissemination of antibiotic resistance genes in the Yellow River basin: focused on family farms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16328-16341. [PMID: 38316741 DOI: 10.1007/s11356-024-32290-5] [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: 10/04/2023] [Accepted: 01/28/2024] [Indexed: 02/07/2024]
Abstract
As an emerging contaminant, antibiotic resistance genes (ARGs) have attracted growing attention, owing to their widespread dissemination and potential risk in the farming environment. However, ARG pollution from family livestock farms in the Yellow River basin, one of the main irrigation water sources in the North China Plain, remains unclear. Herein, we targeted 21 typical family farms to assess the occurrence patterns of ARGs in livestock waste and its influence on ARGs in receiving environment by real-time quantitative PCR (qPCR). Results showed that common ARGs were highly prevalent in family livestock waste, and tet-ARGs and sul-ARGs were the most abundant in these family farms. Most ARG levels in fresh feces of different animals varied, as the trend of chicken farms (broilers > laying hens) > swine farms (piglets > fattening pigs > boars and sows) > cattle farms (dairy cattle > beef cattle). The effect of natural composting on removing ARGs for chicken manure was better than that for cattle manure, while lagoon storage was not effective in removing ARGs from family livestock wastewater. More troublesomely, considerable amounts of ARGs were discharged with manure application, further leading to the ARG increase in farmland soil (up to 58-119 times), which would exert adverse impacts on human health and ecological safety.
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Affiliation(s)
- Shimei Zheng
- College of Chemistry and Chemical and Environmental Engineering, Weifang University, Weifang, 261061, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yandong Wang
- Department of Pediatrics, Weifang People's Hospital, Weifang, 261041, China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Ran Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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Wang Y, Cai J, Chen X, Guo B, Liu J, Qiu G, Li H. The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers. ENVIRONMENTAL RESEARCH 2024; 243:117880. [PMID: 38070858 DOI: 10.1016/j.envres.2023.117880] [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: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jingjing Cai
- Zhejiang Sino-Geo Clean-Soil Company Limited, Zhuji, 311800, China
| | - Xiaodong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bin Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junli Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Gaoyang Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Li T, Xu J, Zhao X, Zhang Q, Zhu T, Fan D, Liu J. Impacts of irrigation with treated livestock wastewater on the accumulation characteristic of ARGs in the farmland soil: a case study in Hohhot, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:26. [PMID: 38225519 DOI: 10.1007/s10653-023-01811-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 01/17/2024]
Abstract
Irrigation with treated livestock wastewater (TWW) is a promising strategy for reusing resources. However, TWW irrigation might introduce antibiotic resistant genes (ARGs) into the soil, posing environmental risks associated with antibiotic resistance. This study focuses on investigating the influence of irrigation amounts and duration on the fate of ARGs and identifies key factors driving their changes. The results showed that there were 13 ARGs in TWW, while only 5 ARGs were detected in irrigated soil. That is some introduced ARGs from TWW could not persistently exist in the soil. After 1-year irrigation, an increase in irrigation amount from 0.016 t/m2 to 0.048 t/m2 significantly enhanced the abundance of tetC by 29.81%, while ermB and sul2 decreased by 45.37% and 76.47%, respectively (p < 0.01). After 2-year irrigation, the abundance of tetC, ermB, ermF, dfrA1, and total ARGs significantly increased (p < 0.05) when the irrigation amount increased. The abundances of ARGs after 2-year irrigation were found to be 2.5-34.4 times higher than 1 year. Obviously, the irrigation years intensified the positive correlation between ARGs abundance and irrigation amount. TetC and ermF were the dominant genes resulting in the accumulation of ARGs. TWW irrigation increased the content of organic matter and total nitrogen in the soil, which affected microbial community structure. The changes of the potential host were the determining factors driving the ARGs abundance. Our study demonstrated that continuous TWW irrigation for 2 years led to a substantial accumulation of ARGs in soil.
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Affiliation(s)
- Tong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Jifei Xu
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China.
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, Inner Mongolia University, Hohhot, 010021, China.
| | - Xiaofang Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Qiuping Zhang
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Tianjiao Zhu
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Deliang Fan
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Jianguo Liu
- College of Energy and Power Engineering, Inner Mongolia University of Technology, Hohhot, 010051, China
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Liu C, Shan X, Song L, Wang J, Chen H. Metagenomics-assembled analysis revealed the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167868. [PMID: 37848139 DOI: 10.1016/j.scitotenv.2023.167868] [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: 09/03/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
Antibiotic resistance has received widespread attention in recent years. Soil irrigation and fertilization are routine agricultural practices, but also lead to the spread of antibiotic resistance genes (ARGs) in soil-crop system such as via resistome coalescence. Despite community coalescence being ubiquitous and important in natural ecosystems, little research has been done to investigate resistome coalescence during soil irrigation activities. In this study, the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials (wastewater, wastewater-river water, and wastewater-manure) have been revealed by utilizing microcosm experiments and high-throughput sequencing-based metagenomic assembly approaches. Results showed irrigation and coalescence changed soil quality and resistome. Totally, 789 unique ARGs were identified in the irrigation system, including some emerging ARGs. The abundance and diversity of ARGs increased in the coalesced soils, mainly due to the newly imported ARGs from irrigation materials. Relatively, the soils irrigated with wastewater and manure showed higher level of ARGs. Irrigation with the mixtures containing river water caused greater loss of indigenous taxa, while the community structure of mixing treatment with manure changed more dramatically. Interestingly, the succession of community in coalesced soils was influenced by transient competition for resources and ecological niche width, and the highest abundance and diversity of microorganisms and ARGs were found in the initial phase of coalescence, followed by a gradual succession towards the original community. With increasement of wastewater in the irrigation materials, the soil community showed a stepwise change rather than linear change. Notably, natural deposit of irrigation materials reduced their impacts on the ARGs in the coalesced soils. Findings provide new insights into the resistome coalescence during agricultural practices for reducing the spread risks of ARGs.
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Affiliation(s)
- Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
| | - Jinsheng Wang
- Advanced Institute of Natural Science, Beijing Normal University at Zhuhai, 519087, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
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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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Wang X, Zhang L, Gu J, Feng Y, He K, Jiang H. Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121950. [PMID: 37279818 DOI: 10.1016/j.envpol.2023.121950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3--N 14.7% and NH4+-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.
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Affiliation(s)
- Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yucheng Feng
- Department of C, rop, Soil & Environmental Sciences (formerly Agronomy and Soils), Auburn University, Auburn, AL36849, USA
| | - Kai He
- Tobacco Monopoly Bureau (Branch), Longhui, Shaoyang, Hunan, 422208, China
| | - Haihong Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Wiesner-Friedman C, Beattie RE, Stewart JR, Hristova KR, Serre ML. Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework. Front Microbiol 2023; 14:1223876. [PMID: 37731922 PMCID: PMC10508347 DOI: 10.3389/fmicb.2023.1223876] [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: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined. Methods To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region. Results A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km. Discussion Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Rachelle E. Beattie
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Jill R. Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Marc L. Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Zhang Y, Cheng D, Xie J, Hu Q, Xie J, Shi X. Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163334. [PMID: 37061064 DOI: 10.1016/j.scitotenv.2023.163334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/01/2023] [Accepted: 04/02/2023] [Indexed: 06/01/2023]
Abstract
Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.
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Affiliation(s)
- Yu Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Jun Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Qijuan Hu
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Jiawei Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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12
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Li Y, Kong F, Li S, Wang J, Hu J, Chen S, Chen Q, Li Y, Ha X, Sun W. Insights into the driving factors of vertical distribution of antibiotic resistance genes in long-term fertilized soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131706. [PMID: 37247491 DOI: 10.1016/j.jhazmat.2023.131706] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in soils has aroused wide attention. However, the influence of long-term fertilization on the distribution of ARGs in different soil layers and its dominant drivers remain largely unknown. In this study, a total of 203 ARGs were analyzed in greenhouse vegetable soils (0-100 cm from a 13-year field experiment applied with different fertilizers (control, chemical fertilizer, organic manure, and mixed fertilizer). Compared with unfertilized and chemically fertilized soils, manure application significantly increased the abundance and alpha diversity of soil ARGs, where the assembly of ARG communities was strongly driven by stochastic processes. The distribution of ARGs was significantly driven by manure application within 60 cm, while it was insignificantly changed in soil below 60 cm under different fertilization regimes. The inter-correlations of ARGs with mobile genetic elements (MGEs) and microbiota were strengthened in manured soil, indicating manure application posed a higher risk for ARGs diffusion in subsurface soil. Bacteria abundance and MGEs directly influenced ARG abundance and composition, whereas soil depth and manure application indirectly influenced ARG abundance and composition by affecting antibiotics. These results strengthen our understanding of the long-term anthropogenic influence on the vertical distribution of soil ARGs and highlight the ecological risk of ARGs in subsurface soil induced by long-term manure application.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Fanguang Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Yantai Institute of China Agricultural University, Yantai 264670, China.
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jingrun Hu
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shuo Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanming Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xuejiao Ha
- Planting Technology Promotion Station of Daxing District, Beijing 102600, China
| | - Weiling Sun
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
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13
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Wei H, Wu D, Zheng M, Wang W, Wang D. Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131443. [PMID: 37094440 DOI: 10.1016/j.jhazmat.2023.131443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.
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Affiliation(s)
- Huawei Wei
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
| | - Dong Wu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Mingying Zheng
- Guizhou Province Bureau of Geology and Mineral Exploration and Development, Guiyang 550004, PR China
| | - Wanjin Wang
- Guizhou Province Bureau of Geology and Mineral Exploration and Development, Guiyang 550004, PR China
| | - Dapeng Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China; Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
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14
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Sun L, Tang D, Tai X, Wang J, Long M, Xian T, Jia H, Wu R, Ma Y, Jiang Y. Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121323. [PMID: 36822312 DOI: 10.1016/j.envpol.2023.121323] [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: 09/02/2022] [Revised: 02/13/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.
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Affiliation(s)
- Likun Sun
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Engineering Research Center for Animal Waste Utilization, Gansu Agricultural University, Lanzhou, 730070, China
| | - Defu Tang
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Xisheng Tai
- College of Urban Environment, Lanzhou City University, China
| | - Jiali Wang
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Min Long
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tingting Xian
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Haofan Jia
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Renfei Wu
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongqi Ma
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yunpeng Jiang
- College of Animal Science, Gansu Agricultural University, Lanzhou, 730070, China
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15
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Mu M, Yang F, Han B, Ding Y, Zhang K. Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161658. [PMID: 36649763 DOI: 10.1016/j.scitotenv.2023.161658] [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: 11/21/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 105-3.57 × 107 copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.
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Affiliation(s)
- Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China.
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China; Key Laboratory of Low-carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs, PR China.
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16
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Guo Y, Qiu T, Gao M, Ru S, Gao H, Wang X. Does increasing the organic fertilizer application rate always boost the antibiotic resistance level in agricultural soils? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121251. [PMID: 36764373 DOI: 10.1016/j.envpol.2023.121251] [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: 11/05/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The amendment of organic fertilizer derived from livestock manure or biosolids is a significant driver of increasing antibiotic resistance in agricultural soils; however, it remains unclear whether increasing organic fertilizer application rates consistently enhances soil antibiotic resistance levels. Herein, we collected soils with long-term amendment with three types of organic fertilizers at four application rates (15, 30, 45, and 60 t/ha/y) and found that the higher the fertilization rate, the higher the antibiotic resistance gene (ARG) abundance. However, when the fertilization rate exceeded 45 t/ha/y, the ARG abundance ceased to significantly increase. Moreover, the soil ARG abundance was positively correlated with total nitrogen (TN) content and bacterial abundance, especially Firmicutes, and negatively affected by pH and bacterial diversity. Soil TN/bacterial abundance and pH/bacterial diversity reached maximum and minimum values at the 45 t/ha/y fertilization rate, respectively. Meanwhile, at this fertilization rate, Firmicutes enrichment peaked. Therefore, an organic fertilization rate of 45 t/ha/y appeared to represent the threshold for soil antibiotic resistance in this study. The underlying mechanism for this threshold was closely related to soil TN, pH, bacterial abundance, and diversity. Taken together, the findings of this study advance the current understanding regarding the soil resistome under different fertilization rates, while also providing novel insights into organic fertilizer management in agricultural practices.
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Affiliation(s)
- Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shuhua Ru
- Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Science, Hebei Fertilizer Technology Innovation Center, Shijiazhuang, 050051, China
| | - Haoze Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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17
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Zhang Y, Hao X, Thomas BW, McAllister TA, Workentine M, Jin L, Shi X, Alexander TW. Soil antibiotic resistance genes accumulate at different rates over four decades of manure application. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130136. [PMID: 36444046 DOI: 10.1016/j.jhazmat.2022.130136] [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: 07/25/2022] [Revised: 09/11/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Manure can be a source of antibiotic resistance genes (ARGs) that enter the soil. However, previous studies assessing ARG persistence in soil have generally lacked continuity over sampling times, consistency of location, and assessing the impact of discontinuing manure application. We evaluated both short- and long-term ARG accumulation dynamics in soil with a 40-year known history of manure use. Manure application caused a greater abundance of tetracycline, macrolide, and sulfonamide ARGs in the soil. There was an initial spike in ARG abundance resulting from manure bacteria harboring ARGs being introduced to soil, followed by resident soil bacteria out-competing them, which led to ARG dissipation within a year. However, over four decades, annual manure application caused linear or exponential ARG accumulation, and bacteria associated with ARGs differed compared to those in the short term. Eleven years after discontinuing manure application, most soil ARG levels declined but remained elevated. We systematically explored the historical accumulation of ARGs in manured soil, and provide insight into factors that affect their persistence.
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Affiliation(s)
- Yuting Zhang
- College of Resources and Environment, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400715, China; Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Xiying Hao
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Ben W Thomas
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC V0M 1A0, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Matthew Workentine
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Long Jin
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Xiaojun Shi
- College of Resources and Environment, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Efficient Utilization of Soil and Fertilizer Resources, State Cultivation Base of Eco-agriculture for Southwest Mountainous Land, Academy of Agriculture Science, Southwest University, Chongqing 400716, China
| | - Trevor W Alexander
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada.
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18
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Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes. Antibiotics (Basel) 2023; 12:antibiotics12020333. [PMID: 36830244 PMCID: PMC9952537 DOI: 10.3390/antibiotics12020333] [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: 12/30/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.
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Tian S, Sun X, Xiao H, Zhou Y, Huang X, An XL, Liu C, Su JQ. Evaluation of rice straw and its transformation products on norfloxacin degradation and antibiotic resistome attenuation during soil incorporation. CHEMOSPHERE 2023; 313:137451. [PMID: 36464023 DOI: 10.1016/j.chemosphere.2022.137451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Straw incorporation into reclaimed soils has been demonstrated to increase soil nutrients and has the potential to efficiently increase crop production. However, which incorporation mode is more helpful in the control of antibiotic resistance genes (ARGs) remains unknown. In this study, we systematically compared the occurrence of antibiotic resistome in norfloxacin contaminated soils amended with rice straw (RS) and the transformation products, biochar (RSB) and ash (RSA). RS significantly promoted the degradation of norfloxacin (0.0648 d-1, 3 times faster than control), whereas RSB had little effect and RSA hindered the degradation. Based on metagenomic analysis, RS and RSB significantly reduced the ARGs relative abundance (0.1421 and 0.1991 compared to 0.2540 in control) at the end of soil incubation. Adonis test indicated that all of amendment treatments significantly affect the microbial communities in soils, whereas only RS and RSB significantly affect the variation of antibiotic resistome. Procrustes analysis confirmed the association of microbial communities and ARGs. Network analysis further revealed that the reduction in Actinobacteria was the main reason for the general decrease of ARGs relative abundance during soil incorporation, whereas Proteobacteria and Bacteroidetes were responsible for temporary promotion of ARGs in RS and RSB at the early stage. Finally, scientifically setting up the usage of rice straw and optimizing the preparation process of biochar are suggested for the synchronous control of the risk of antibiotics and ARGs during soil incorporation.
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Affiliation(s)
- Shaohua Tian
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Xuecong Sun
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Hai Xiao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Yanyan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Xu Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China.
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Chaoxiang Liu
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, 350108, PR China.
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
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20
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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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21
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Wang P, Ding L, Li F, Liao J, Wang M. Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities. PeerJ 2022; 10:e14314. [PMID: 36389419 PMCID: PMC9653066 DOI: 10.7717/peerj.14314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Although the effects of herbivore camping on soil physicochemical properties have been studied, whether the effects alter the soil microbial communities (e.g., composition, functions, taxonomic and functional diversities, network) remain unknown, especially below the surface. Here, using paired subsoil samples from half month-camping and non-camping, we showed for the first time that camping significantly changed the relative abundance of 21 bacterial phylotypes and five fungal phylotypes. Specifically, we observed significant increases in the relative abundance of putative chitinase and terpenes vanillin-decomposition genes, nitrite reduction function (nirB, nasA), decreases in the relative abundance of putative carbon fixation genes (ackA, PGK, and Pak), starch-decomposition gene (dexB), gene coding nitrogenase (anfG), and tetracycline resistance gene (tetB) for bacterial communities, and significant decreases in the relative abundance of animal endosymbiont and increases in the relative abundance of litter saprotroph and endophyte for fungal communities. However, camping did not significantly impact the taxonomic and functional diversity. The niche restriction was the main driving force of bacterial and fungal community assembly. Compared to no camping, camping increased the stability of bacterial networks but decreased the stability of fungal networks. Camping exerted a positive effect on the network by compressing the niche width and reduced the change in the network by reducing the niche overlap. Our results suggest that camping restructures the soil microbial composition, function, and network, and provides a novel insight into the effect of animal camping on soil microbial communities in grassland.
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Affiliation(s)
- Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, The People’s Republic of China
| | - Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, The People’s Republic of China
| | - Fuxiang Li
- Guizhou Weining plateau Grassland Experimental Station, Weining, Guizhou, The People’s Republic of China
| | - Jiafa Liao
- Guizhou Weining plateau Grassland Experimental Station, Weining, Guizhou, The People’s Republic of China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, Guizhou, The People’s Republic of China
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22
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Zhang H, Ling H, Zhou R, Tang J, Hua R, Wu X. Contrasting dynamics of manure-borne antibiotic resistance genes in different soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114162. [PMID: 36252512 DOI: 10.1016/j.ecoenv.2022.114162] [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: 06/15/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance genes (ARGs) are important biological contamination factors in soil systems, posing direct or indirect threats to soil health, food safety and human health. The ubiquitous pollution of ARGs is usually implicated with the application of organic manures in agricultural soil ecosystem. However, little is known about the transmission and fate of ARGs after manure input concerning different soils. Herein, the transmission potential and temporal dynamics of manure-associated ARGs was characterized with three different agricultural soils collected from Jiangxi (JX), Zhejiang (ZJ), and Jilin (JL), respectively. The results show that manure input did not affect the total abundance of ARGs in the receiving soils, but remarkedly alter the compositions of ARGs in soils. The manure-associated ARGs were significantly enriched in the manure-amended soils, including genes conferring resistance to sulfonamide, aminoglycoside, tetracycline, chloramphenicol, and trimethoprim with the fold of 1.97 - 27.86. Variance partitioning analysis showed that the major variances of ARG community was explained by mobile genetic elements and bacterial profile (> 76%) but not the concentrations of heavy metals and antibiotics. Furthermore, 31, 37, and 38 ARG subtypes were identified as the potential extrinsic ARGs derived from manures in the JX, ZJ, and JL soils, respectively, including 13 shared ARG subtypes. It was also found that the manure-associated ARGs (aadA, sul1, sul2, tetC, and tetG) declined with the incubation time in the JX and ZJ soils, whereas they firstly decreased and then increased in the JL soil. The abundance of these five ARGs in the JL soil was significantly higher than that in the JX and ZJ soils. Collectively, this finding revealed that soil type was responsible for the transmission and fate of manure-associated ARGs in agroecosystem.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Hong Ling
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Ruofei Zhou
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China.
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23
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Li T, Li R, Cao Y, Tao C, Deng X, Ou Y, Liu H, Shen Z, Li R, Shen Q. Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129704. [PMID: 36104920 DOI: 10.1016/j.jhazmat.2022.129704] [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: 05/01/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.
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Affiliation(s)
- Tingting Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Ruochen Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yifan Cao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
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24
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Wang Q, Huang Q, Liu Y, Khan MA, Guo G, Lu W, Li X, Hu S, Wang J. Temporal variation of the coupling relationship between methanogens and biogeochemical process in soil-microbes-rice system. CHEMOSPHERE 2022; 303:135099. [PMID: 35618072 DOI: 10.1016/j.chemosphere.2022.135099] [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: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Microbial community were most resilient option for methane associated mitigation strategies. Biogas slurry provides plant nutrition and affects microbial community. However, little is known about the changes of the functional guilds (methanogen and methanotroph) in the geochemical context after addition biogas slurry. For this purpose, a pot experiment was conducted. Six treatment groups were included in this study, four with biogas slurry: water ratio (1:4, T02; 2:3, T04; 3:2, T06; 4:1, T08), one with a chemical fertilizer (F), and a control (CK). The effective tiller and biomass significantly increased by 1.9 times and 2.1 times in T02 relative to CK. The relative abundance of Bacteroidetes in the biogas slurry treatments was 31.5%, while that in CK was 11.4%. The dominant methanogens in CK, F and treatments were different at heading and mature stages. CK and F were hydrogenotrophs with relative abundance of 0.09% and 0.06%, and the treatment group was acetotrophs with mean value of 1.21% at heading stage. Compared with CK, the number of methanotrophs in the treatments at heading stage increased by 4.1 times, while that at mature increased by 10.3 times. The methanogenic community in the treatments may be shaped by the amount of biogas slurry applied rather than by biogeochemical processes at heading stage. Nevertheless, there may be existed synergistic interaction in the soil-microbes-rice system at mature stage. These findings may provide a better understanding of regulating soil respiration in agricultural land.
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Affiliation(s)
- Qingqing Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Qing Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Yin Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Muhammad Amjad Khan
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Genmao Guo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Wenkang Lu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Xiaohui Li
- Hainan Inspection and Detection Center for Modern Agriculture, Haikou, Hainan, 570100, China
| | - Shan Hu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Junfeng Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
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25
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Zhang Y, Cheng D, Xie J, Zhang Y, Wan Y, Zhang Y, Shi X. Impacts of farmland application of antibiotic-contaminated manures on the occurrence of antibiotic residues and antibiotic resistance genes in soil: A meta-analysis study. CHEMOSPHERE 2022; 300:134529. [PMID: 35395269 DOI: 10.1016/j.chemosphere.2022.134529] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/23/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
A meta-analysis of 94 published studies was conducted to explore the impacts of farmland application of antibiotic-contaminated manures on antibiotic concentrations and ARG abundances in manure-amended soil. Forty-nine antibiotics were reported, in which chlortetracycline, oxytetracycline, doxycycline, tetracycline, enrofloxacin, ciprofloxacin and norfloxacin were the most prevalent and had relatively high concentrations. The responses of ARG and mobile genetic element (MGE) abundances to farmland application of antibiotic-contaminated manures varied considerably under different management strategies and environmental settings. On average, compared to unamended treatments, farmland application of antibiotic-contaminated manures significantly increased the total ARG and MGE abundances by 591% and 351%, respectively (P < 0.05). Of all the included ARG classes, the largest increase was found for sulfonamide resistance genes (1121%), followed by aminoglycoside (852%) and tetracycline (763%) resistance genes. Correlation analysis suggested that soil organic carbon (SOC) was significantly negatively correlated with antibiotic concentrations in manured soil (P < 0.05) due to the formation of covalent bonds and nonextractable residues. Soil silt content was significantly positively correlated with antibiotic concentration (P < 0.05), which was attributed to greater sorption capacities. The ARG abundances were significantly positively correlated with soil silt content, antibiotic concentrations, mean annual temperature, SOC, MGEs and soil pH (P < 0.05), suggesting that changes in these factors may shape the ARG profiles. Collectively, these findings advanced our understanding of the occurrence of antibiotics and ARGs in manure-amended soil and potential factors affecting them and will contribute to better management of these contaminants in future agricultural production.
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Affiliation(s)
- Yu Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Jun Xie
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Yuting Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Yu Wan
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yueqiang Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing, 400716, China.
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26
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Mu M, Yang F, Han B, Tian X, Zhang K. Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 237:113555. [PMID: 35483148 DOI: 10.1016/j.ecoenv.2022.113555] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 - 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of blaampC showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p>0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., blaampC, blaTEM-1) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.
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Affiliation(s)
- Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xueli Tian
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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27
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Zhou G, Tao HB, Wen X, Wang YS, Peng H, Liu HZ, Yang XJ, Huang XM, Shi QS, Xie XB. Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals. CHEMOSPHERE 2022; 291:132766. [PMID: 34740703 DOI: 10.1016/j.chemosphere.2021.132766] [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: 06/17/2021] [Revised: 09/26/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.
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Affiliation(s)
- Gang Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hong-Bing Tao
- Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xia Wen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Ying-Si Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hong Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hui-Zhong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiu-Jiang Yang
- Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiao-Mo Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China; Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Qing-Shan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiao-Bao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
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28
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Jadeja NB, Worrich A. From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches. Environ Microbiol 2022; 24:3290-3306. [PMID: 35172395 DOI: 10.1111/1462-2920.15927] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.
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Affiliation(s)
- Niti B Jadeja
- Ashoka Trust for Research in Ecology and the Environment, PO, Royal Enclave, Srirampura, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Anja Worrich
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, 04318, Germany
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29
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Li H, Zheng X, Tan L, Shao Z, Cao H, Xu Y. The vertical migration of antibiotic-resistant genes and pathogens in soil and vegetables after the application of different fertilizers. ENVIRONMENTAL RESEARCH 2022; 203:111884. [PMID: 34400159 DOI: 10.1016/j.envres.2021.111884] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 05/28/2023]
Abstract
The prevalence of bacterial resistance caused by the application of animal manure has become an important environmental issue. Herein, the vertical migration of antibiotic resistance genes (ARGs) and pathogens in soil and vegetables after the application of different fertilizers was explored. The results showed that the application of composted manure considerably enhanced the abundance of most ARGs and pathogens, especially in surface soil and pakchoi roots. Moreover, the soil ARGs increased partially from log 1.93 to log 4.65 after the application of composted manure, and six pathogens were simultaneously detected. It was observed that the increase in soil depth decreased most ARGs and pathogens by log 1.04-2.24 and 53.98 %~85.54 %, respectively. This indicated that ARGs and pathogens still existed in the deep soil (80-100 cm). Moreover, total organic carbon had a significant influence on the pathogen distribution, whereas bacterial communities primarily drove the vertical migration of ARGs rather than environmental factors. Although most of the ARG-host associations observed in the surface soil were disappeared in deep soil as revealed by network analysis, some co-occurrence pattern still occurred in deep soil, suggesting that some ARGs might be carried to deep soil by their host bacteria. These results were novel in describing the vertical migration of ARGs in the environment after the application of different fertilizers, providing ideas for curbing their migration to crops.
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Affiliation(s)
- Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Zhenlu Shao
- Shan Dong Agriculture University, Tai' An, 271018, China
| | - Haoyu Cao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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