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Peng J, Wang D, He P, Wei P, Zhang L, Lan W, Zhang X, Guan J, Chen Y, Li W, Zheng Y, Li Y, Chen W, Zhao Z, Jiang L, Zhou L. Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks. ENVIRONMENTAL RESEARCH 2024; 257:119298. [PMID: 38823616 DOI: 10.1016/j.envres.2024.119298] [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: 04/18/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/03/2024]
Abstract
Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.
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Affiliation(s)
- Jinxia Peng
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Dapeng Wang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pingping He
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Pinyuan Wei
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Li Zhang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Wenlu Lan
- Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Marine Environmental Monitoring Centre of Guangxi, Beihai, 536000, China
| | - Xingzhi Zhang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Junliang Guan
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yongxian Chen
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Wei Li
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yusi Zheng
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yusen Li
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Wenjian Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Linyuan Jiang
- China(Guangxi)-ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Lei Zhou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Hou Y, Diao W, Jia R, Sun W, Feng W, Li B, Zhu J. Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem. ENVIRONMENTAL RESEARCH 2024; 251:118717. [PMID: 38518910 DOI: 10.1016/j.envres.2024.118717] [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: 11/30/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.
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Affiliation(s)
- Yiran Hou
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Weixu Diao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Rui Jia
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wei Sun
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Bing Li
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
| | - Jian Zhu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
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Wang H, Wang X, Zhang L, Zhang X, Cao Y, Xiao R, Bai Z, Ma L. Meta-analysis addressing the potential of antibiotic resistance gene elimination through aerobic composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 182:197-206. [PMID: 38670003 DOI: 10.1016/j.wasman.2024.04.034] [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: 11/06/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The significant increase in antibiotic resistance genes (ARGs) in organic solid wastes (OSWs) has emerged as a major threat to the food chain. Aerobic composting is a widely used technology for OSW management, with the potential to influence the fate of AGRs. However, the variability of the ARG elimination effects reported in different studies has highlighted the uncertainty regarding the effects of composting on ARGs. To identify the potential of composting in reducing ARG and the factors (e.g., composting technologies and physiochemical properties) influence ARG changes, a meta-analysis was conducted with a database including 4,232 observations. The abundances of ARGs and mobile genetic elements (MGEs) can be substantially reduced by 74.3% and 78.8%, respectively, via aerobic composting. During composting, the ARG levels in chicken and swine manure tended to be reduced more significantly (81.7% and 78.0%) compared to those in cattle manure (52.3%) and sewage sludge (32.6%). The reduction rate of sulfonamide resistant genes was only 35.3%, which was much lower than those of other types. MGEs and composting duration (CD) were identified as the most important factors driving ARG changes during composting. These findings provide a comprehensive insight into the effects of composting on ARG reduction, which may help prevent the transmission in food systems.
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Affiliation(s)
- Hongge Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Xuan Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Xinyuan Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Yubo Cao
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Ran Xiao
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhaohai Bai
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Lin Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China.
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Wang S, Nie W, Gu Q, Wang X, Yang D, Li H, Wang P, Liao W, Huang J, Yuan Q, Zhou S, Ahmad I, Kotaro K, Chen G, Zhu B. Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database. WATER RESEARCH 2024; 256:121572. [PMID: 38621316 DOI: 10.1016/j.watres.2024.121572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.
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Affiliation(s)
- Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Qing Gu
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Xie Wang
- Southwest China Mountain Agricultural Environment Key Laboratory, Ministry of Agriculture and Rural Areas, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Shizishan Rd, Chengdu, 610066, China
| | - Danping Yang
- Observation and Research Station of Ecological Restoration for Chongqing Typical Mining Areas, Ministry of Natural Resources (Chongqing Institute of Geology and Mineral Resources), Chongqing, 401120. China
| | - Hongyu Li
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Huang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Quan Yuan
- School of Energy and Power Engineering, Xihua University, Chengdu, 610039, China
| | - Shengli Zhou
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Kiga Kotaro
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Fang C, Su Y, Zhuo Q, Wang X, Ma S, Zhan M, He X, Huang G. Responses of greenhouse gas emissions to aeration coupled with functional membrane during industrial-scale composting of dairy manure: Insights into bacterial community composition and function. BIORESOURCE TECHNOLOGY 2024; 393:130079. [PMID: 37993066 DOI: 10.1016/j.biortech.2023.130079] [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: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
Greenhouse gas (GHG) emissions from manure management processes deserve more attention. Using three industrial-scale experiments, this study comprehensively evaluated the effects of different aeration coupled with semi-permeable membrane-covered strategies on the structure and function of bacterial communities and their impact on GHG emissions during dairy manure aerobic composting. The succession of the bacterial communities tended to be consistent for similar aeration strategies. Ruminiclostridium and norank_f__MBA03 were significantly positively correlated with the methane emission rate, and forced aeration coupled with semi-permeable membrane-covered decreased GHG emissions by inhibiting these taxa. Metabolism was the most active function of the bacterial communities, and its relative abundance accounted for 75.69%-80.23%. The combined process also enhanced carbohydrate metabolism and amino acid metabolism. Therefore, forced aeration coupled with semi-permeable membrane-covered represented a novel strategy for reducing global warming potential by regulating the structure and function of the bacterial communities during aerobic composting of dairy manure.
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Affiliation(s)
- Chen Fang
- College of Agriculture, Guizhou University, Guiyang, Guizhou Province 550025, China; Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Ya Su
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Qianting Zhuo
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoli Wang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Shuangshuang Ma
- Institute of Energy and Environmental Protection, Academy of Agricultural Planning & Engineering, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Muqing Zhan
- College of Agriculture, Guizhou University, Guiyang, Guizhou Province 550025, China
| | - Xueqin He
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Guangqun Huang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
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Ahmed I, Zhang Y, Sun P, Xie Y, Zhang B. Sensitive response mechanism of ARGs and MGEs to initial designed temperature during swine manure and food waste co-composting. ENVIRONMENTAL RESEARCH 2023; 216:114513. [PMID: 36208781 DOI: 10.1016/j.envres.2022.114513] [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: 08/07/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
The rapid aerobic composting process has been used to reduce organic wastes, but the associated risks of antibiotic resistance genes (ARGs) need to evaluate in an efficient way. The primary objective of this work was to explore the underlying mechanism of initial adjustment in composting temperature on the variation of ARGs, mobile genetic elements (MGEs), and microbial composition during co-composting. The co-composting was initially externally heated (T2) for 5 days. The results showed that ARGs abundance in conventional composting (T1) was reduced by 49.36%, while multidrug was enriched by 86.16% after a period of 30 days. While in T2 ARGs were removed by 79.46% particularly the fraction of sulfonamide, multidrug, and vancomycin resistance genes were >90% without rebounding of any ARGs. Whereas, MGEs were reduced by 68.12% and 93.62% in T1 and T2, while the half-lives of ARGs and MGEs were lower in T2 compared to T1 (86.3%,86.7%). T2 also affected the metabolism function by regulating carbohydrate metabolism (9.62-10.39%) and amino acid metabolism (9.92-10.93%). Apart from this, the potential human pathogenic bacteria Pseudomonas was reduced by 90.6% in T2 and only 32.9% in T1 respectively. Network analysis showed that Ureibacillus, Weissella, Corynebacterium, Escherichia-Shigella, Acinetobacter were the main host of multiple genes. Structural equation models exhibited that bacterial communities were mainly responsible for the enrichment of ARGs in T1, whereas, it was directly affected by MGEs in T2. Similarly, ARGs variation was directly related to composting temperature. With this simple strategy, ARGs associated risk can be significantly reduced in composting.
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Affiliation(s)
- Imtiaz Ahmed
- School of Environmental Science and Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yongpeng Zhang
- School of Environmental Science and Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Pengyu Sun
- School of Environmental Science and Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yu Xie
- School of Environmental Science and Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Bo Zhang
- School of Environmental Science and Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai, 200240, China.
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Yang Y, Li L, Huang F, Hu X, Cao X, Mi J, Liao X, Xing S. The fate of antibiotic resistance genes and their association with bacterial and archaeal communities during advanced treatment of pig farm wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158364. [PMID: 36041618 DOI: 10.1016/j.scitotenv.2022.158364] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Advanced wastewater treatment plants are widely used in most large-scale pig farms in southern China. However, the fate of antibiotic resistance genes (ARGs) and their association with bacterial and archaeal communities during advanced wastewater treatment remain unclear. In this study, the profiles of ARGs in typical advanced wastewater treatment plants were surveyed using metagenomic analysis. The results showed that 279- 326 different subtypes of ARGs were detected in raw wastewater, with a total abundance of 5.98 ± 0.48 copies per bacterial cell. During the advanced wastewater treatment, the abundance and number of ARGs were significantly reduced. Microbial communities (bacteria and archaea) contributed the most to the variation in ARG abundance and composition (PCA axis_1), accounting for 10.8 % and 15.7 %, respectively, followed by mobile genetic elements (MGEs) and physicochemical factors. Special attention should be given to potential pathogenic bacteria such as Escherichia, Streptococcus, Enterococcus and Staphylococcus and archaea such as Methanocorpusculum, Candidatus Methanoplasma and Candidatus Methanomethylophilus, which were important potential ARG hosts. Bacterial communities may indirectly affect ARG variation by affecting archaeal communities. These findings indicated that ARG levels in pig farm wastewater can be effectively reduced during advanced treatment and highlighted the important role played by archaea, which should not be ignored.
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Affiliation(s)
- Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Linfei Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Feng Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xinwen Hu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xinwei Cao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sicheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
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Guan Y, Jia J, Fan X, Li K, Wang Z. Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106221. [PMID: 35709638 DOI: 10.1016/j.aquatox.2022.106221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.
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Affiliation(s)
- Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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9
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Yang J, Tong C, Xiao D, Xie L, Zhao R, Huo Z, Tang Z, Hao J, Zeng Z, Xiong W. Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes. Microbiol Spectr 2022; 10:e0190721. [PMID: 35230155 PMCID: PMC9045286 DOI: 10.1128/spectrum.01907-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/24/2022] [Indexed: 01/14/2023] Open
Abstract
The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.
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Affiliation(s)
- Jintao Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Cuihong Tong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Danyu Xiao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ruonan Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Huo
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziyun Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jie Hao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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10
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Wang C, Zhu W, Strong PJ, Zhu F, Han X, Hong C, Wang W, Yao Y. Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14732-14745. [PMID: 34689552 DOI: 10.1021/acs.est.1c03933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.
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Affiliation(s)
- Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Weijing Zhu
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, GPO Box 2432, 2 George St, Brisbane, QLD 4001, Australia
| | - Fengxiang Zhu
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Chunlai Hong
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Weiping Wang
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yanlai Yao
- Institute of Environmental Resources and Soil Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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11
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Liu B, Yu K, Ahmed I, Gin K, Xi B, Wei Z, He Y, Zhang B. Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148372. [PMID: 34139488 DOI: 10.1016/j.scitotenv.2021.148372] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.
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Affiliation(s)
- Botao Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Imtiaz Ahmed
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Gin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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12
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Ezugworie FN, Igbokwe VC, Onwosi CO. Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147191. [PMID: 33905939 DOI: 10.1016/j.scitotenv.2021.147191] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 05/28/2023]
Abstract
Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.
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Affiliation(s)
- Flora N Ezugworie
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Victor C Igbokwe
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chukwudi O Onwosi
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria.
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13
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Tang X, Shen M, Zhang Y, Zhu D, Wang H, Zhao Y, Kang Y. The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities. CHEMOSPHERE 2021; 266:128985. [PMID: 33228990 DOI: 10.1016/j.chemosphere.2020.128985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.
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Affiliation(s)
- Xingyao Tang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Min Shen
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yanzhou Zhang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Dewei Zhu
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Huanli Wang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yongqiang Zhao
- Yancheng National Nature Reserve for Rare Birds, Yancheng, Jiangsu, PR China
| | - Yijun Kang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China.
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14
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Li K, Cao R, Mo S, Yao R, Ren Z, Wu J. Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community. Front Microbiol 2020; 11:592592. [PMID: 33250880 PMCID: PMC7673438 DOI: 10.3389/fmicb.2020.592592] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 103 to 1.13 × 108 copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.
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Affiliation(s)
- Ke Li
- College of Animal Sciences and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Cao
- College of Animal Sciences and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shangkun Mo
- College of Animal Sciences and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rensheng Yao
- Animal Husbandry and Veterinary Station of Guangling District, Yangzhou, China
| | - Zhuqing Ren
- College of Animal Sciences and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jian Wu
- College of Animal Sciences and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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15
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Ding J, Wei D, An Z, Zhang C, Jin L, Wang L, Li Y, Li Q. Succession of the bacterial community structure and functional prediction in two composting systems viewed through metatranscriptomics. BIORESOURCE TECHNOLOGY 2020; 313:123688. [PMID: 32590304 DOI: 10.1016/j.biortech.2020.123688] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/13/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
In this work, Illumina MiSeq sequencing of cDNA from metatranscriptomics RNA reverse transcription were employed in combination with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to estimate the dynamic variations of bacterial community structures and metabolic functions in a bioreactor and traditional composting process. Results showed that the change of bacterial α-diversity in the first three stages exhibit opposite trends in the two composting systems. The four most abundant phyla were the same in both systems (Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria), but the most abundant genera were different. The five most abundant genus-level groups in the bioreactor were Psychrobacter, Galbibacter, Pseudomonas, Staphylococcus and Flavobacterium. Within the same phase, the functional bacteria were dramatically different in the two composting processes. In the bioreactor system both bacterial community structure and metabolism function were greatly affected by available phosphorus.
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Affiliation(s)
- Jianli Ding
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Zhizhuang An
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chengjun Zhang
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Liang Jin
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lei Wang
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yan Li
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qiao Li
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events. Vet Sci 2020; 7:vetsci7030110. [PMID: 32823495 PMCID: PMC7558842 DOI: 10.3390/vetsci7030110] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/26/2022] Open
Abstract
The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.
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