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Zhang Y, Chen W, Yuan Y, Liao X, Mi J. Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175275. [PMID: 39111271 DOI: 10.1016/j.scitotenv.2024.175275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wenbo Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Institute of Marine Science, University of Auckland, Auckland, 1010, New Zealand
| | - Yilin Yuan
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730000, China.
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2
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Zhou Y, Li Q. Preference and regulation mechanism mediated via mobile genetic elements for antibiotic and metal resistomes during composting amended with nano ZVI loaded on biochar. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124520. [PMID: 38992827 DOI: 10.1016/j.envpol.2024.124520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
This study assessed the effectiveness of nano zero-valent iron loaded on biochar (BC-nZVI) during swine manure composting. BC-nZVI significantly reduced the abundance of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). BC-nZVI modified the preference of MGEs to carry ARGs and MRGs, and the corrosion products of BC-nZVI could destroy cell structure, hinder electron transfer between cells, and weaken the association between ARGs, MRGs, and host bacteria. Functional genes analysis revealed that BC-nZVI down-regulated the abundance of genes affecting the transmission and metabolism of ARGs and MRGs, including type IV secretion systems, transporter systems, two-component systems, and multidrug efflux pumps. Furthermore, the BC-nZVI decreased genes related to flagella and pili production and cell membrane permeability, thereby hindering the transfer of ARGs, MRGs, and MGEs in the environment. Redundancy analysis demonstrated that changes in the microbial community induced by BC-nZVI were pivotal factors impacting the abundance of ARGs, MRGs, and MGEs. Overall, this study confirmed the efficacy of BC-nZVI in reducing resistance genes during swine manure composting, offering a promising environmental strategy to mitigate the dissemination of these contaminants.
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Affiliation(s)
- Yucheng Zhou
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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3
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Wang X, Li J, Pan X. How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173881. [PMID: 38871331 DOI: 10.1016/j.scitotenv.2024.173881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.
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Affiliation(s)
- Xiaonan Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Hangzhou 310015, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou 221116, China; Shaoxing Research Institute of Zhejiang University of Technology, Shaoxing 312000, China
| | - Jiahao Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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4
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Sun B, Bai Z, Li R, Song M, Zhang J, Wang J, Zhuang X. Efficient elimination of antibiotic resistome in livestock manure by semi-permeable membrane covered hyperthermophilic composting. BIORESOURCE TECHNOLOGY 2024; 407:131134. [PMID: 39038713 DOI: 10.1016/j.biortech.2024.131134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Livestock manure is a hotspot for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and an important contributor to antibiotic resistance in non-clinical settings. This study investigated the effectiveness and potential mechanisms of a novel composting technology, semi-permeable membrane covered hyperthermophilic composting (smHTC), in removal of ARGs and MGEs in chicken manure. Results showed that smHTC was more efficient in removal of ARGs and MGEs (92% and 93%) compared to conventional thermophilic composting (cTC) (76% and 92%). The efficient removal in smHTC is attributed to direct or indirect negative effects caused by the high temperature, including reducing the involvement of bio-available heavy metals (HMs) in co-selection processes of antibiotic resistance, decreasing the bacterial abundance and diversity, suppressing the horizontal gene transfer and killing potential ARGs hosts. Overall, smHTC can efficiently remove the resistome in livestock manure, reducing the risk to crops and humans from ARGs residues in compost products.
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Affiliation(s)
- Bo Sun
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Xiongan Innovation Institute, Xiongan New Area, Hebei 071000, China.
| | - Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Manjiao Song
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhang
- Binzhou Institute of Technology, Binzhou, Shandong 256606, China
| | - Jiancheng Wang
- Binzhou Institute of Technology, Binzhou, Shandong 256606, China.
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 102699, China.
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5
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Su Z, Cui S, Wen D, Chen L. Metagenomic insights into resistome, mobilome and virulome in different fecal waste. ENVIRONMENTAL RESEARCH 2024; 262:119861. [PMID: 39208976 DOI: 10.1016/j.envres.2024.119861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Fecal waste is a significant source of antimicrobial resistance (AMR) pollution and provides valuable insights into the AMR development in animal and human populations within the "One health" framework. Various genetic elements, including antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs), are crucial AMR risk determinants (ARDs). However, few studies focused on compositional characteristics of ARDs in different feces. Here, we analyzed 753 public metagenomes from human, pig, chicken, and cattle feces, revealing significant differences in ARD richness and abundance across fecal types, notably lowest in cattle samples. Tetracycline, multi-metal, and -biocide resistance genes were dominant resistome. A few core genes contributed to 25.6%-91.1% of gene abundance, and their correlations were stronger in cattle samples. Procrustes analysis showed that microbial composition had higher correlations with ARGs (M2 = 0.579) and BMGs (M2 = 0.519). Gammaproteobacteria was identified as major ARD-hosts especially in human and pig feces, and they mainly carried multi-resistance genes. MGEs exhibited direct positive effects on ARGs and BMGs, indirectly impacting VFGs. Utilizing random forest methods, we identified 42 indicator genes for tracking AMR pollution originating from fecal sources in the environments. This study offers new insights into understanding and controlling the AMR pollution of fecal waste from human and food animals.
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Affiliation(s)
- Zhiguo Su
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Saishi Cui
- Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Lyujun Chen
- School of Environment, Tsinghua University, Beijing 100084, China.
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6
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Pan Y, Zeng J, Zhang L, Hu J, Hao H, Zeng Z, Li Y. The fate of antibiotics and antibiotic resistance genes in Large-Scale chicken farm Environments: Preliminary view of the performance of National veterinary Antimicrobial use reduction Action in Guangdong, China. ENVIRONMENT INTERNATIONAL 2024; 191:108974. [PMID: 39186902 DOI: 10.1016/j.envint.2024.108974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/24/2024] [Accepted: 08/19/2024] [Indexed: 08/28/2024]
Abstract
In 2018, China implemented the Veterinary Antimicrobial Use Reduction Action to curb the rapid development of antibiotic resistance (AR). However, the AR-related pollutions in animal farms after the reduction policy has been poorly investigated. Here, we performed a comprehensive investigation combining UPLC-MS/MS, metagenomic, and bacterial genomic analyses in eight representative large-scale chicken farms in Guangdong, China. Our results showed that antibiotics and ARGs contaminations were more severe in broiler farms than in layer farms. Notably, diverse tet(X) variants were prevalent in the chicken farms. These tet(X)s was carried by diverse E. coli lineages and obviously correlated with ISCR2 and IS1B transposases. The resistomes in chicken farms was significantly correlated with microbial community, and multiple factor analyses indicated that the joint effect of antibiotics-microbial community-MGEs was the most dominant driver of ARGs. Host tracking identified a variety of ARG bacterial hosts and the co-occurrence of ARGs-MRGs-MGEs. Source tracking indicated that the inherent component represented the main feature of resistomes in different hosts, while ARG transfer between the chicken gut and farm environments were frequent. A multiperspective evaluation of AR risk revealed that the early effect of antibiotic reduction was exhibited by the mitigation of maximum level of risky ARGs, prevalence of environmental AR pathogens, and HGT potential of ARGs mediated by phage structures. Overall, our findings provide insights into the antibiotic and ARG profiles in large-scale chicken farms with different rearing strategies and demonstrate a preliminary view of the performance of antibiotic reduction actions in China.
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Affiliation(s)
- Yu Pan
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; College of Animal Science and Technology, State International Joint Research Center for Animal Health Breeding, Shihezi University, Shihezi 832003, China
| | - Jiaxiong Zeng
- 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
| | - Lingxuan Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jianxin Hu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Haihong Hao
- College of Animal Science and Technology, State International Joint Research Center for Animal Health Breeding, Shihezi University, Shihezi 832003, China; National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenling Zeng
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China.
| | - Yafei Li
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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7
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Wang Z, Fu Y, Zheng YL, Jiang N, Jiang H, Wu C, Lv Z, Krüger-Haker H, Feßler AT, Schwarz S, Wang Y. Fate of florfenicol and linezolid resistance genes and their bacterial hosts during two waste treatment models in swine feedlots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173645. [PMID: 38821272 DOI: 10.1016/j.scitotenv.2024.173645] [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: 02/28/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.
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Affiliation(s)
- Zheng Wang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China.
| | - Yulin Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Central Laboratory Department, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yong-Liang Zheng
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
| | - Nansong Jiang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Haiyang Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziquan Lv
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Henrike Krüger-Haker
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Schwarz
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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8
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Rosberg AK, Silva MJ, Skøtt Feidenhans’l C, Cytryn E, Jurkevitch E, Lood R. Regulation of Antibiotic Resistance Genes on Agricultural Land Is Dependent on Both Choice of Organic Amendment and Prevalence of Predatory Bacteria. Antibiotics (Basel) 2024; 13:750. [PMID: 39200050 PMCID: PMC11350732 DOI: 10.3390/antibiotics13080750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/28/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024] Open
Abstract
Antibiotic resistance genes (ARGs) are widespread in the environment, and soils, specifically, are hotspots for microorganisms with inherent antibiotic resistance. Manure and sludge used as fertilizers in agricultural production have been shown to contain vast amounts of ARGs, and due to continued applications, ARGs accumulate in agricultural soils. Some soils, however, harbor a resilience capacity that could depend on specific soil properties, as well as the presence of predatory bacteria that are able to hydrolyse living bacteria, including bacteria of clinical importance. The objectives of this study were to (i) investigate if the antibiotic resistance profile of the soil microbiota could be differently affected by the addition of cow manure, chicken manure, and sludge, and (ii) investigate if the amendments had an effect on the presence of predatory bacteria. The three organic amendments were mixed separately with a field soil, divided into pots, and incubated in a greenhouse for 28 days. Droplet digital PCR (ddPCR) was used to quantify three ARGs, two predatory bacteria, and total number of bacteria. In this study, we demonstrated that the choice of organic amendment significantly affected the antibiotic resistance profile of soil, and promoted the growth of predatory bacteria, while the total number of bacteria was unaffected.
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Affiliation(s)
- Anna Karin Rosberg
- Microbial Horticulture Laboratory, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, 234 56 Alnarp, Sweden;
| | - Maria João Silva
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 84 Lund, Sweden;
| | | | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, P.O. Box 15159, Rishon LeZion 7528809, Israel;
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Rolf Lood
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 84 Lund, Sweden;
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9
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Cui E, Zhou Z, Cui B, Fan X, Ali Abid A, Chen T, Gao F, Du Z. Effects of nitrogen fertilization on the fate of high-risk antibiotic resistance genes in reclaimed water-irrigated soil and plants. ENVIRONMENT INTERNATIONAL 2024; 190:108834. [PMID: 38908278 DOI: 10.1016/j.envint.2024.108834] [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: 11/27/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
High-risk antibiotic resistance genes (ARGs) in reclaimed water-irrigated soil pose a potential threat to ecosystem and human health. Inorganic fertilization - including with nitrogen, a key ingredient in agricultural production - may affect the ARG profile in soil. However, little is known about nitrogen fertilization's influence on ARGs profiles in the soil-plant system. This study investigated the effects of different nitrogen fertilizer types (CO(NH2)2, NO3--N (NaNO3) and NH4+-N (NH4HCO3)) and different nitrogen fertilizer application rates (low, medium, high) on the distribution of high-risk ARGs in reclaimed water-irrigated soil and plants using quantitative PCR, high-throughput sequencing and metagenomic sequencing. Soil microcosms results revealed that nitrogen fertilization significantly affected the pattern of high-risk ARGs in soil, and also affected high-risk ARGs abundance and transfer capacity in plants. Compared with nitrogen fertilizer application rate, nitrogen fertilizer types significantly contributed to enhancing the soil resistome, with the order of CO(NH2)2 > NO3--N ≈ NH4+-N. The medium application of NO3--N and NH4+-N significantly reduced high-risk ARGs abundance in the leaf endophyte. Bacterial community mainly drove the variation of ARGs in nitrogen-fertilized soil-plant system, and class I integron and metal resistance genes (MRGs) also had direct effects on these high-risk ARGs. A similar high-risk ARGs pattern was also found in field plot experiments, and several dangerous pathogens were observed as the main high-risk ARGs potential hosts in nitrogen-fertilized soil. Based on an economic assessment, application of NH4+-N (NH4HCO3) could reduce costs by $1,312.83 ha-1 compared with NO3--N (NaNO3). These results showed that the more important role of nitrogen type might be an effective and economical way to control high-risk ARGs spread in soil-plant system under reclaimed water irrigation.
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Affiliation(s)
- Erping Cui
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100000, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bingjian Cui
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
| | - Abbas Ali Abid
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Hangzhou 310058, China
| | - Taotao Chen
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100000, China
| | - Feng Gao
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Zhenjie Du
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
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10
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Wang G, Gao X, Cai Y, Li G, Ma R, Yuan J. Dynamics of antibiotic resistance genes during manure composting: Reduction in herbivores manure and accumulation in carnivores. ENVIRONMENT INTERNATIONAL 2024; 190:108900. [PMID: 39053194 DOI: 10.1016/j.envint.2024.108900] [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: 04/10/2024] [Revised: 06/17/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The elevated levels of antibiotic resistance genes (ARGs) in livestock manure represent a significant threat to both the environment and human health. Composting has been recognized as an effective strategy to mitigate the abundance of ARGs in manure. However, notable rebounds in ARGs abundance have been observed during this process. This study explored the changes in ARGs abundance and the underlying influencing factors during the composting of carnivore (chicken and pig) and herbivore (sheep and cow) manures, along with mushroom residues. The findings revealed that the total relative abundance of ARGs increased by 6.96 and 10.94 folds in chicken and pig manure composts, respectively, whereas it decreased by a remarkable 91.72% and 98.37% in sheep and cow manure composts. Nitrogen content emerged as the primary physicochemical factors governing the abundance of ARGs in chicken and pig manure composts. Conversely, carbon content played a pivotal role in determining ARGs abundance in chicken and pig manure composts. Furthermore, the presence of dominant hosts, such as Corynebacterium, Bacillus, and Clostridium, along with emerging bacteria like Thermobifida, Saccharomonospora, and Actinomadura, contributed significantly to the enrichment of total ARGs, including tetG, tetO, tetX, and sul2, in chicken and pig manure composts. The coexistence of these genes with mobile genetic elements and a plethora of host bacteria, coupled with their high abundance, renders them particularly high-risk ARGs. On the other hand, the observed decrease in the abundance of total ARGs in sheep and cow manure composts can be attributed to the decline in the population of host bacteria, specifically Atopostipes, Psychrobacter, and Corynebacterium. Collectively, these results provide crucial insights into the management of ARGs risks and offer essential theoretical support for enhancing the safe utilization of organic fertilizer in agriculture.
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Affiliation(s)
- Guoying Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China.
| | - Xia Gao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yu Cai
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ruonan Ma
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China.
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11
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Checcucci A, Buscaroli E, Modesto M, Luise D, Blasioli S, Scarafile D, Di Vito M, Bugli F, Trevisi P, Braschi I, Mattarelli P. The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116774. [PMID: 39053184 DOI: 10.1016/j.ecoenv.2024.116774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/18/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.
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Affiliation(s)
- Alice Checcucci
- Dipartimento di Scienze e Tecnologie Agrarie, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Enrico Buscaroli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy.
| | - Monica Modesto
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy.
| | - Diana Luise
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Sonia Blasioli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Donatella Scarafile
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Maura Di Vito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy; Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paolo Trevisi
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Ilaria Braschi
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Paola Mattarelli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
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12
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Gao Z, Cao M, Ma S, Geng H, Li J, Xu Q, Sun K, Wang F. Sulfadiazine proliferated antibiotic resistance genes in the phycosphere of Chlorella pyrenoidosa: Insights from bacterial communities and microalgal metabolites. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134679. [PMID: 38795485 DOI: 10.1016/j.jhazmat.2024.134679] [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: 02/29/2024] [Revised: 04/30/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
The phycosphere is an essential ecological niche for the proliferation of antibiotic resistance genes (ARGs). However, how ARGs' potential hosts change and the driving mechanism of metabolites under antibiotic stress in the phycosphere have seldom been researched. We investigated the response of Chlorella pyrenoidosa and the structure and abundance of free-living (FL) and particle-attached (PA) bacteria, ARGs, and metabolites under sulfadiazine by using real-time quantitative PCR, 16 S rRNA high-throughput. The linkage of key bacterial communities, ARGs, and metabolites through correlations was established. Through analysis of physiological indicators, Chlorella pyrenoidosa displayed a pattern of "low-dose promotion and high-dose inhibition" under antibiotic stress. ARGs were enriched in the PA treatment groups by 117 %. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria as potential hosts for ARGs. At the genus level, potential hosts included Sphingopyxis, SM1A02, Aquimonas, Vitellibacter, and Proteiniphilum. Middle and high antibiotic concentrations induced the secretion of metabolites closely related to potential hosts by algae, such as phytosphingosine, Lysophosphatidylcholine, and α-Linolenic acid. Therefore, changes in bacterial communities indirectly influenced the distribution of ARGs through alterations in metabolic products. These findings offer essential details about the mechanisms behind the spread and proliferation of ARGs in the phycosphere.
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Affiliation(s)
- Ziqi Gao
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China
| | - Manman Cao
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China
| | - Shuai Ma
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China.
| | - Huanhuan Geng
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Junhong Li
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Qing Xu
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China
| | - Ke Sun
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China
| | - Fei Wang
- School of Environment, Beijing Normal University, 19 Xinjiekouwai Street, Beijing 100875, China.
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13
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Pires AJ, Pereira G, Fangueiro D, Bexiga R, Oliveira M. When the solution becomes the problem: a review on antimicrobial resistance in dairy cattle. Future Microbiol 2024; 19:903-929. [PMID: 38661710 PMCID: PMC11290761 DOI: 10.2217/fmb-2023-0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Antibiotics' action, once a 'magic bullet', is now hindered by widespread microbial resistance, creating a global antimicrobial resistance (AMR) crisis. A primary driver of AMR is the selective pressure from antimicrobial use. Between 2000 and 2015, antibiotic consumption increased by 65%, reaching 34.8 billion tons, 73% of which was used in animals. In the dairy cattle sector, antibiotics are crucial for treating diseases like mastitis, posing risks to humans, animals and potentially leading to environmental contamination. To address AMR, strategies like selective dry cow therapy, alternative treatments (nanoparticles, phages) and waste management innovations are emerging. However, most solutions are in development, emphasizing the urgent need for further research to tackle AMR in dairy farms.
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Affiliation(s)
- Ana José Pires
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477, Lisbon, Portugal
| | - Gonçalo Pereira
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477, Lisbon, Portugal
| | - David Fangueiro
- LEAF Research Center, Terra Associate Laboratory, Instituto Superior de Agronomia, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Ricardo Bexiga
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477, Lisbon, Portugal
| | - Manuela Oliveira
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477, Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477, Lisbon, Portugal
- cE3c—Centre for Ecology, Evolution & Environmental Changes & CHANGE—Global Change & Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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14
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Ma W, An B, Xu X, Huo M, Mi K, Tian X, Kou Z, Tang A, Cheng G, Huang L. Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting. ENVIRONMENTAL RESEARCH 2024; 252:119033. [PMID: 38685300 DOI: 10.1016/j.envres.2024.119033] [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: 06/14/2023] [Revised: 03/14/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.
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Affiliation(s)
- Wenjin Ma
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Boyu An
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiangyue Xu
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Meixia Huo
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Kun Mi
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyuan Tian
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Ziyan Kou
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Aoran Tang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Guyue Cheng
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
| | - Lingli Huang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
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15
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He L, Wang Y, Xi B, Zhao X, Cai D, Sun Y, Du Y, Zhang C. Synergistic removal of total petroleum hydrocarbons and antibiotic resistance genes in Yellow River Delta wetlands contaminated soil composting regulated by biogas slurry addition. ENVIRONMENTAL RESEARCH 2024; 252:118724. [PMID: 38518917 DOI: 10.1016/j.envres.2024.118724] [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: 01/29/2024] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
The interactive effects between the emerging contaminant antibiotic resistance genes (ARGs) and the traditional pollutant total petroleum hydrocarbons (TPHs) in contaminated soils remain unclear. The synergistic removal of TPHs and ARGs from composted contaminated soil, along with the microbial mechanisms driven by the addition of biogas slurry, have not yet been investigated. This study explored the impact of biogas slurry on the synergistic degradation mechanisms and bacterial community dynamics of ARGs and TPHs in compost derived from contaminated soil. The addition of biogas slurry resulted in a reduction of targeted ARGs and mobile genetic elements (MGEs) by 9.96%-95.70% and 13.32%-97.66%, respectively. Biogas slurry changed the succession of bacterial communities during composting, thereby reducing the transmission risk of ARGs. Pseudomonas, Cellvibrio, and Devosia were identified as core microorganisms in the synergistic degradation of ARGs and TPHs. According to the partial least squares path model, temperature and NO3- indirectly influenced the removal of ARGs and TPHs by directly regulating the abundance and composition of host microbes and MGEs. In summary, the results of this study contribute to the high-value utilization of biogas slurry and provide methodological support for the low-cost remediation of contaminated soils.
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Affiliation(s)
- Liangzi He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541000, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Danmei Cai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yiwen Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yuewei Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Chuanyan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; School of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541000, China
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16
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Zhang R, Gong C, Liu M, Zhou L, Zhuang H, Hu Z. High-throughput profiling the effects of zinc on antibiotic resistance genes in the anaerobic digestion of swine manure. ENVIRONMENTAL TECHNOLOGY 2024; 45:3315-3327. [PMID: 37193677 DOI: 10.1080/09593330.2023.2215452] [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: 11/19/2022] [Accepted: 03/25/2023] [Indexed: 05/18/2023]
Abstract
The problem of antibiotic resistance genes (ARGs) caused by heavy metals has attracted extensive attention of human beings. Zn, a widely used feed additive, has a very high residue in swine manure, but the distribution characteristics of ARGs imposed by Zn in anaerobic digestion (AD) products are not clear. In this study, the behaviour of mobile genetic elements (MGEs), bacterial community, and their association with ARGs were determined in the presence of 125 and 1250 mg L-1 Zn in AD system of swine manure. Zn-treated enriched the abundance of ARGs, and produced some new genotypes that were not detected in CK treatment. In addition, low concentration of Zn significantly increased the relative abundance of ARGs, as compared to higher Zn and CK group. Correspondingly, the abundances of most top30 genus were highest in ZnL (125 mg L-1 Zn), followed by CK and ZnH (1250 mg L-1 Zn). Notably, network analysis showed that the relationship between ARGs and MGEs is closer than that ARGs and bacteria, suggesting that ARGs increased in Zn-treated, especially low level Zn, may be due to the amplification transfer of ARGs among varied microorganisms by horizontal transfer with MGEs. Therefore, strengthen the management of in livestock manure is crucial to control the spread of ARGs in organic fertilizers.
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Affiliation(s)
- Ranran Zhang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, People's Republic of China
| | - Chenpan Gong
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
| | - Menglong Liu
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
| | - Liuyuan Zhou
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
| | - Haifeng Zhuang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
| | - Zhijun Hu
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, People's Republic of China
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17
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Im D, Chen Y, Nishimura F. Effects of hydrothermal treatment on the reduction of antibiotic-resistant Escherichia coli and antibiotic resistance genes and the fertilizer potential of liquid product from cattle manure. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 183:123-131. [PMID: 38744164 DOI: 10.1016/j.wasman.2024.05.006] [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: 09/19/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
In this study, the reduction in the abundance of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) and the fertilizer potential of liquid products from hydrothermally treated cattle manure were investigated. Hydrothermal treatment (HTT) was conducted under different reaction temperatures (125, 150, 175 and 200 °C) and retention times (60, 90 and 120 min). The total organic carbon (TOC) and total nitrogen (TN) of the liquid product increased with increasing reaction temperature. The germination index (GI), a measure of the percentage of germination, exceeded 90 % at 125, 150, and 175 °C in diluted samples, while it decreased to 18 % at 200 °C. Although a longer retention time contributed to an increase in TOC of liquid products, it did not increase the GI values. The liquid product should be diluted or adjusted before use as fertilizer to prevent phytotoxicity. In our analysis of ARB and ARGs, E. coli and antibiotic-resistant E. coli were completely reduced after HTT, except for the operating conditions of 125 °C and 60 min. Although both a higher reaction temperature and longer retention time tended to be better for the reduction of ARGs and intI1, it was found that the longer retention time is much more effective than the higher reaction temperature. The reduction of target ARGs and intI1 was 2.9-log under175 °C and 120 min. Comprehensively considering the fertilizer potential of liquid product and the reduction of ARB and ARGs, 175 °C of reaction temperature and 120 min of retention time of operating conditions for HTT were recommended.
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Affiliation(s)
- Dongbeom Im
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan.
| | - Yiren Chen
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Fumitake Nishimura
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
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18
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Liu W, Xie WY, Liu HJ, Chen C, Chen SY, Jiang GF, Zhao FJ. Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172558. [PMID: 38643884 DOI: 10.1016/j.scitotenv.2024.172558] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56% and 4-45% of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hong-Jun Liu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Chen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-Yao Chen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Gao-Fei Jiang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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19
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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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20
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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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21
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Lei L, Chen N, Chen Z, Zhao Y, Lin H, Li X, Hu W, Zhang H, Shi J, Luo Y. Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms. WATER RESEARCH 2024; 256:121584. [PMID: 38598950 DOI: 10.1016/j.watres.2024.121584] [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: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.
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Affiliation(s)
- Liusheng Lei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Nan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Zeyou Chen
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Yirong Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Huai Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Xi Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Wenjin Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hanhui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Jingliang Shi
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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22
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He D, Li J, Yu W, Zhang Y, Wang B, Wang T, Yang H, Zhang Y, Chen W, Li Y, Feng F, Hou LA. Deciphering the removal of antibiotics and the antibiotic resistome from typical hospital wastewater treatment systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171806. [PMID: 38508266 DOI: 10.1016/j.scitotenv.2024.171806] [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: 01/03/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Hospital wastewater treatment systems (HWTSs) are a significant source and reservoir of antibiotic resistance genes (ARGs) and a crucial hub for transmitting ARGs from clinical to natural environments. However, there is a lack of research on the antibiotic resistome of clinical wastewater in HWTSs. In this study, we used metagenomics to analyze the prevalence and abundance of ARGs in five typical HWTSs. A total of 17 antibiotics from six categories were detected in the five HWTSs; β-lactam antibiotics were found at the highest concentrations, with up to 4074.08 ng·L-1. We further found a total of 21 ARG types and 1106 subtypes of ARGs with the highest percentage of multi-drug resistance genes (evgS, msbA, arlS, and baeS). The most abundant last-resort ARGs were mcr, which were detected in 100 % of the samples. HWTSs effluent is a major pathway for the transmission of last-resort ARGs into urban wastewater networks. The removal of antibiotics, antibiotic-resistant bacteria, and ARGs from HWTSs was mainly achieved by tertiary treatment, i.e., chlorine disinfection, but antibiotics and ARGs were still present in the HWTSs effluent or even increased after treatment. Moreover, antibiotics and heavy metals (especially mercury) in hospital effluents can exert selective pressure for antibiotic resistance, even at low concentrations. Qualitative analyses based on metagenome-assembled genome analysis revealed that the putative hosts of the identified ARGs are widely distributed among Pseudomonas, Acidovorax, Flavobacterium, Polaromonas, and Arcobacter. Moreover, we further assessed the clinical availability of ARGs and found that multidrug ARGs had the highest clinical relevance values. This study provides new impulses for monitoring and removing antibiotics and ARGs in the hospital sewage treatment process.
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Affiliation(s)
- Dahai He
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China.
| | - Weihai Yu
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Yingyuan Zhang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China; Guizhou Academy of Testing and Analysis, Guiyang 550000, China
| | - Bin Wang
- College of Civil Engineering, Guizhou University, Guiyang 550025, China
| | - Tao Wang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
| | - Huaikai Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Yuntao Zhang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Weijie Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 550025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang 550025, China
| | - Faming Feng
- Chutian Liangjiang Environment Co., LTD, Guiyang 550000, China
| | - Li-An Hou
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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23
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Jiang L, Dai J, Wang L, Chen L, Zeng G, Liu E, Zhou X, Yao H, Xiao Y, Fang J. Ca(H 2PO 4) 2 and MgSO 4 activated nitrogen-related bacteria and genes in thermophilic stage of compost. Appl Microbiol Biotechnol 2024; 108:331. [PMID: 38734749 PMCID: PMC11088556 DOI: 10.1007/s00253-024-13167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
This study was conducted to investigate the effects of Ca(H2PO4)2 and MgSO4 on the bacterial community and nitrogen metabolism genes in the aerobic composting of pig manure. The experimental treatments were set up as control (C), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), and 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2), which were used at the end of composting for potting trials. The results showed that Ca(H2PO4)2 and MgSO4 played an excellent role in retaining nitrogen and increasing the alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of the composts. Adding Ca(H2PO4)2 and MgSO4 changed the microbial community structure of the compost. The microorganisms associated with nitrogen retention were activated. The complexity of the microbial network was enhanced. Genetic prediction analysis showed that the addition of Ca(H2PO4)2 and MgSO4 reduced the accumulation of nitroso-nitrogen and the process of denitrification. At the same time, despite the reduction of genes related to nitrogen fixation, the conversion of ammonia to nitrogenous organic compounds was promoted and the stability of nitrogen was increased. Mantel test analysis showed that Ca(H2PO4)2 and MgSO4 can affect nitrogen transformation-related bacteria and thus indirectly affect nitrogen metabolism genes by influencing the temperature, pH, and organic matter (OM) of the compost and also directly affected nitrogen metabolism genes through PO43- and Mg2+. The pot experiment showed that composting with 1.5% Ca(H2PO4)2 + 3% MgSO4 produced the compost product that improved the growth yield and nutrient content of cilantro and increased the fertility of the soil. In conclusion, Ca(H2PO4)2 and MgSO4 reduces the loss of nitrogen from compost, activates nitrogen-related bacteria and genes in the thermophilic phase of composting, and improves the fertilizer efficiency of compost products. KEY POINTS: • Ca(H2PO4)2 and MgSO4 reduced the nitrogen loss and improved the compost effect • Activated nitrogen-related bacteria and altered nitrogen metabolism genes • Improved the yield and quality of cilantro and fertility of soil.
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Affiliation(s)
- Lihong Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China
| | - Jiapeng Dai
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lutong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Guangxi Zeng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Erlun Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiangdan Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Hao Yao
- Board of Directors Department, Changsha IMADEK Intelligent Technology Company Limited, Changsha, 410137, China
| | - Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China.
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China.
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24
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Yu X, Lv Y, Wang Q, Wang W, Wang Z, Wu N, Liu X, Wang X, Xu X. Deciphering and predicting changes in antibiotic resistance genes during pig manure aerobic composting via machine learning model. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33610-33622. [PMID: 38689043 DOI: 10.1007/s11356-024-33087-2] [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: 01/03/2024] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Livestock manure is one of the most important pools of antibiotic resistance genes (ARGs) in the environment. Aerobic composting can effectively reduce the spread of antibiotic resistance risk in livestock manure. Understanding the effect of aerobic composting process parameters on manure-sourced ARGs is important to control their spreading risk. In this study, the effects of process parameters on ARGs during aerobic composting of pig manure were explored through data mining based on 191 valid data collected from literature. Machine learning (ML) models (XGBoost and Random Forest) were utilized to predict the rate of ARGs changes during pig manure composting. The model evaluation index of the XGBoost model (R2 = 0.651) was higher than that of the Random Forest (R2 = 0.490), indicating that XGBoost had better prediction performance. Feature importance was further calculated for the XGBoost model, and the XGBoost black box model was interpreted by Shapley additive explanations analysis. Results indicated that the influencing factors on the ARGs variation in pig manure were sequentially divided into thermophilic period, total composting period, composting real time, and thermophilic stage average temperature. The findings gave an insight into the application of ML models to predict and decipher the ARG changes during manure composting and provided suggestions for better composting manipulation and optimization of process parameters.
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Affiliation(s)
- Xiaohui Yu
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Yang Lv
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Qing Wang
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Wenhao Wang
- College of Chemical Engineering and Material Science, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiqiang Wang
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Nan Wu
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China.
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China.
| | - Xinyuan Liu
- College of Engineering and Technology, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xiaobo Wang
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China
- College of Agronomy and Resource and Environment, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xiaoyan Xu
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Tianjin Agricultural University, Tianjin, 300392, China
- College of Agronomy and Resource and Environment, Tianjin Agricultural University, Tianjin, 300392, China
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25
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Stehling EG, Furlan JPR, Lopes R, Chodkowski J, Stopnisek N, Savazzi EA, Shade A. The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123849. [PMID: 38522607 DOI: 10.1016/j.envpol.2024.123849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.
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Affiliation(s)
- Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
| | - John Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University (MSU) - East Lansing, United States.
| | - Nejc Stopnisek
- Department of Microbiology and Molecular Genetics, Michigan State University (MSU) - East Lansing, United States; National Laboratory of Health, Environment and Food - Maribor, Slovenia.
| | | | - Ashley Shade
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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26
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de Oliveira AR, de Toledo Rós B, Jardim R, Kotowski N, de Barros A, Pereira RHG, Almeida NF, Dávila AMR. A comparative genomics study of the microbiome and freshwater resistome in Southern Pantanal. Front Genet 2024; 15:1352801. [PMID: 38699231 PMCID: PMC11063290 DOI: 10.3389/fgene.2024.1352801] [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: 12/08/2023] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
This study explores the resistome and bacterial diversity of two small lakes in the Southern Pantanal, one in Aquidauana sub-region, close to a farm, and one in Abobral sub-region, an environmentally preserved area. Shotgun metagenomic sequencing data from water column samples collected near and far from the floating macrophyte Eichhornia crassipes were used. The Abobral small lake exhibited the highest diversity and abundance of antibiotic resistance genes (ARGs), antibiotic resistance classes (ARGCs), phylum, and genus. RPOB2 and its resistance class, multidrug resistance, were the most abundant ARG and ARGC, respectively. Pseudomonadota was the dominant phylum across all sites, and Streptomyces was the most abundant genus considering all sites.
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Affiliation(s)
- André R. de Oliveira
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nelson Kotowski
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | | | - Alberto M. R. Dávila
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
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27
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Daw Elbait G, Daou M, Abuoudah M, Elmekawy A, Hasan SW, Everett DB, Alsafar H, Henschel A, Yousef AF. Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater. PLoS One 2024; 19:e0298325. [PMID: 38578803 PMCID: PMC10997137 DOI: 10.1371/journal.pone.0298325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/18/2024] [Indexed: 04/07/2024] Open
Abstract
Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.
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Affiliation(s)
- Gihan Daw Elbait
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed Elmekawy
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Shadi W. Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dean B. Everett
- Department of Pathology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F. Yousef
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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Li L, Liu X, Li J, Chen Z, Song T, Jin S, Zhu C, Luo L, Geng B, Zhu J. Mitigating Tetracycline antibiotic contamination in chicken manure using ex situ fermentation system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120614. [PMID: 38513588 DOI: 10.1016/j.jenvman.2024.120614] [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: 10/27/2023] [Revised: 02/21/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
Excessive use of tetracycline antibiotics in poultry farming results in significant concentrations of these drugs and tetracycline resistance genes (TRGs) in chicken manure, impacting both environmental and human health. Our research represents the first investigation into the removal dynamics of chlortetracycline (CTC) and TRGs in different layers of an ex situ fermentation system (EFS) for chicken waste treatment. By pinpointing and analyzing dominant TRGs-harboring bacteria and their interactions with environmental variables, we've closed an existing knowledge gap. Findings revealed that CTC's degradation half-lives spanned 3.3-5.8 days across different EFS layers, and TRG removal efficiency ranged between 86.82% and 99.52%. Network analysis highlighted Proteobacteria and Actinobacteria's essential roles in TRGs elimination, whereas Chloroflexi broadened the potential TRG hosts in the lower layer. Physical and chemical conditions within the EFS influenced microbial community diversity, subsequently impacting TRGs and integrons. Importantly, our study reports that the middle EFS layer exhibited superior performance in eliminating CTC and key TRGs (tetW, tetG, and tetX) as well as intI2. Our work transcends immediate health and environmental remediation by offering insights that encourage sustainable agriculture practices.
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Affiliation(s)
- Luyao Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xue Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jiabin Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhuobo Chen
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Tingting Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shan Jin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Liangguo Luo
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Bing Geng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Jie Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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29
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Wu X, Nawaz S, Li Y, Zhang H. Environmental health hazards of untreated livestock wastewater: potential risks and future perspectives. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:24745-24767. [PMID: 38499926 DOI: 10.1007/s11356-024-32853-6] [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: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Due to technological and economic limitations, waste products such as sewage and manure generated in livestock farming lack comprehensive scientific and centralized treatment. This leads to the exposure of various contaminants in livestock wastewater, posing potential risks to both the ecological environment and human health. This review evaluates the environmental and physical health risks posed by common pollutants in livestock wastewater and outlines future treatment methods to mitigate these risks. Residual wastes in livestock wastewater, including pathogenic bacteria and parasites surviving after epidemics or diseases on various farms, along with antibiotics, organic wastes, and heavy metals from farming activities, contribute to environmental damage and pose risks to human health. As the livestock industry's development increasingly impacts society's future negatively, addressing the issue of residual wastes in livestock wastewater discharge becomes imperative. Ongoing advancements in wastewater treatment systems are consistently updating and refining practices to effectively minimize waste exposure at the discharge source, mitigating risks to environmental ecology and human health. This review not only summarizes the "potential risks of livestock wastewater" but also explores "the prospects for the development of wastewater treatment technologies" based on current reports. It offers valuable insights to support the long-term and healthy development of the livestock industry and contribute to the sustainable development of the ecological environment.
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Affiliation(s)
- Xiaomei Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Shah Nawaz
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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30
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Wen X, Chen M, Ma B, Xu J, Zhu T, Zou Y, Liao X, Wang Y, Worrich A, Wu Y. Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 177:76-85. [PMID: 38290350 DOI: 10.1016/j.wasman.2024.01.037] [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: 09/23/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Majian Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ting Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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31
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Jiang L, Dai J, Wang L, Chen L, Zeng G, Liu E, Zhou X, Yao H, Xiao Y, Fang J. Effect of nitrogen retention composite additives Ca(H 2PO 4) 2 and MgSO 4 on the degradation of lignocellulose, compost maturation, and fungal communities in compost. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-32992-w. [PMID: 38558335 DOI: 10.1007/s11356-024-32992-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
This study investigated the effects of the nitrogen retention composite additives Ca(H2PO4)2 and MgSO4 on lignocellulose degradation, maturation, and fungal communities in composts. The study included control (C, without Ca(H2PO4)2 and MgSO4), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2). The results showed that Ca(H2PO4)2 and MgSO4 enhanced the degradation of total organic carbon (TOC) and promoted the degradation of lignocellulose in compost, with CaPM2 showing the highest TOC and lignocellulose degradation. Changes in the three-dimensional excitation-emission matrix fluorescence spectroscopy (3D-EEM) of dissolved organic matter (DOM) components in compost indicated that the treatment group with the addition of Ca(H2PO4)2 and MgSO4 promoted the production of humic acids (HAs) and increased the degree of compost decomposition, with CaPM2 demonstrating the highest degree of decomposition. The addition of Ca(H2PO4)2 and MgSO4 modified the composition of the fungal community. Ca(H2PO4)2 and MgSO4 increased the relative abundance of Ascomycota, decreased unclassified_Fungi, and Glomeromycota, and activated the fungal genera Thermomyces and Aspergillus, which can degrade lignin and cellulose during the thermophilic stage of composting. Ca(H2PO4)2 and MgSO4 also increased the abundance of Saprotroph, particularly undefined Saprotroph. In conclusion, the addition of Ca(H2PO4)2 and MgSO4 in composting activated fungal communities involved in lignocellulose degradation, promoted the degradation of lignocellulose, and enhanced the maturation degree of compost.
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Affiliation(s)
- Lihong Jiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China
| | - Jiapeng Dai
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lutong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Guangxi Zeng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Erlun Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiangdan Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Hao Yao
- Board of Directors Department, Changsha IMADEK Intelligent Technology Company Limited, Changsha, 410137, China
| | - Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
- Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha, 410128, China.
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32
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Xue W, Shi X, Guo J, Wen S, Lin W, He Q, Gao Y, Wang R, Xu Y. Affecting factors and mechanism of removing antibiotics and antibiotic resistance genes by nano zero-valent iron (nZVI) and modified nZVI: A critical review. WATER RESEARCH 2024; 253:121309. [PMID: 38367381 DOI: 10.1016/j.watres.2024.121309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
Antibiotics and antibiotic resistance genetic pollution have become a global environmental and health concern recently, with frequent detection in various environmental media. Therefore, finding ways to control antibiotics and antibiotic resistance genes (ARGs) is urgently needed. Nano zero-valent iron (nZVI) has shown a positive effect on antibiotics degradation and restraining ARGs, making it a promising solution for controlling antibiotics and ARGs. However, given the current increasingly fragmented research focus and results, a comprehensive review is still lacking. In this work, we first introduce the origin and transmission of antibiotics and ARGs in various environmental media, and then discuss the affecting factors during the degradation of antibiotics and the control of ARGs by nZVI and modified nZVI, including pH, nZVI dose, and oxidant concentration, etc. Then, the mechanisms of antibiotic and ARGs removal promoted by nZVI are also summarized. In general, the mechanism of antibiotic degradation by nZVI mainly includes adsorption and reduction, while promoting the biodegradation of antibiotics by affecting the microbial community. nZVI can also be combined with persulfates to degrade antibiotics through advanced oxidation processes. For the control of ARGs, nZVI not only changes the microbial community structure, but also affects the proliferation of ARGs through affecting the fate of mobile genetic elements (MGEs). Finally, some new ideas on the application of nZVI in the treatment of antibiotic resistance are proposed. This paper provides a reference for research and application in this field.
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Affiliation(s)
- Wenjing Xue
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaoyu Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Jiaming Guo
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Siqi Wen
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Weilong Lin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Qi He
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Yang Gao
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha 410114, PR China
| | - Rongzhong Wang
- School of Resource & Environment and Safety Engineering, University of South China, Heng yang 421001, PR China
| | - Yiqun Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225009, PR China.
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33
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Zhao R, Han B, Yang F, Zhang Z, Sun Y, Li X, Liu Y, Ding Y. Analysis of extracellular and intracellular antibiotic resistance genes in commercial organic fertilizers reveals a non-negligible risk posed by extracellular genes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120359. [PMID: 38359629 DOI: 10.1016/j.jenvman.2024.120359] [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: 09/19/2023] [Revised: 01/12/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Livestock manure is known to be a significant reservoir of antibiotic resistance genes (ARGs), posing a major threat to human health and animal safety. ARGs are found in both intracellular and extracellular DNA fractions. However, there has been no comprehensive analysis of these fractions in commercial organic fertilizers (COFs). The present study conducted a systematic survey of the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) and their contributing factor in COFs in Northern China. Results showed that the ARG diversity in COFs (i.e., 57 iARGs and 53 eARGs) was significantly lower than that in cow dung (i.e., 68 iARGs and 69 eARGs). The total abundance of iARGs and eARGs decreased by 85.7% and 75.8%, respectively, after compost processing, and there were no significant differences between iARGs and eARGs in COFs (P > 0.05). Notably, the relative abundance of Campilobacterota decreased significantly (99.1-100.0%) after composting, while that of Actinobacteriota and Firmicutes increased by 21.1% and 29.7%, respectively, becoming the dominant bacteria in COFs. Co-occurrence analysis showed that microorganisms and mobile genetic elements (MGEs) were more closely related to eARGs than iARGs in COFs. And structural equation models (SEMs) further verified that microbial community was an essential factor regulating iARGs and eARGs variation in COFs, with a direct influence (λ = 0.74 and 0.62, P < 0.01), following by similar effects of MGEs (λ = 0.59 and 0.43, P < 0.05). These findings indicate the need to separate eARGs and iARGs when assessing the risk of dissemination and during removal management in the environment.
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Affiliation(s)
- Ran Zhao
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Bingjun Han
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Zulin Zhang
- The James Hutton Institute, Aberdeen AB15 8QH, UK
| | - Yutao Sun
- Tianjin Zhongtao Earthworm Breeding Professional Cooperative, Tianjin 300191, China
| | - Xue Li
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yiming Liu
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yongzhen Ding
- China-UK Agro-Environmental Pollution Prevention and Control Joint Research Centre, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, 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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Liu S, Zeng JL, Cheng ZW, He JL, Pang YL, Liao XD, Xing SC. Evaluation of compost quality and the environmental effects of semipermeable membrane composting with poultry manure using sawdust or mushroom residue as the bulking agent. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 353:120162. [PMID: 38310794 DOI: 10.1016/j.jenvman.2024.120162] [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: 11/07/2023] [Revised: 01/05/2024] [Accepted: 01/20/2024] [Indexed: 02/06/2024]
Abstract
Herein, the effects of different bulking agents (sawdust and mushroom residue), on compost quality and the environmental benefits of semipermeable film composting with poultry manure were investigated. The results show that composting with sawdust as the bulking agent resulted in greater efficiency and more cost benefits than composting with mushroom residue, and the cost of sawdust for treating an equal volume of manure was only 1/6 of that of mushroom residue. Additionally, lignin degradation and potential carbon emission reduction in the sawdust group were better than those in the mushroom residue group, and the lignin degradation efficiency of the bottom sample in the sawdust group was 48.57 %. Coupling between lignin degradation and potential carbon emission reduction was also closer in sawdust piles than in mushroom residue piles, and sawdust is more environmentally friendly. The abundance of key functional genes was higher at the bottom of each pile relative to the top and middle. Limnochordaceae, Lactobacillus and Enterococcus were the core microorganisms involved in coupling between lignin degradation and potential carbon emission reduction, and the coupled relationship was influenced by electric conductivity, ammonia nitrogen and total nitrogen in the compost piles. This study provides important data for supporting bulking agent selection in semipermeable film composting and for improving the composting process. The results have high value for compost production and process application.
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Affiliation(s)
- Shuo Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jing-Li Zeng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zeng-Wen Cheng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jun-Liang He
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yan-Li Pang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xin-Di Liao
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China
| | - Si-Cheng Xing
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou, 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, 510642, Guangdong, China.
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36
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Yu Y, Zhang Q, Kang J, Xu N, Zhang Z, Deng Y, Gillings M, Lu T, Qian H. Effects of organic fertilizers on plant growth and the rhizosphere microbiome. Appl Environ Microbiol 2024; 90:e0171923. [PMID: 38193672 PMCID: PMC10880660 DOI: 10.1128/aem.01719-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yu Deng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, New South Wales, Australia
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, China
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37
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Li T, Tao S, Ma M, Liu S, Shen M, Zhang H. Is the application of organic fertilizers becoming an undeniable source of microplastics and resistance genes in agricultural systems? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169571. [PMID: 38142997 DOI: 10.1016/j.scitotenv.2023.169571] [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: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
The application of organic fertilizers is becoming an undeniable source of microplastics and antibiotic resistance genes (ARGs) in agricultural soils. The complex microbial activity further transfers resistance genes and their host bacteria to agricultural products and throughout the entire food chain. Therefore, the current main focus is on reducing the abundance of microplastics and ARGs in organic fertilizers at the source, as well as managing microplastics and ARGs in soil. The control of microplastic abundance in organic fertilizers is currently only achieved through pre-composting selection and other methods. However, there are still many shortcomings in the research on the distribution characteristics, propagation and diffusion mechanisms, and control technologies of ARGs, and some key scientific issues still need to be urgently addressed. The high-temperature composting of organic waste can effectively reduce the abundance of ARGs in organic fertilizers to a certain extent. However, it is also important to consider the spread of ARGs in residual antibiotic-resistant bacteria (ARB). This article systematically explores the pathways and interactions of microplastics and resistance genes entering agricultural soils through the application of organic fertilizers. The removal of microplastics and ARGs from organic fertilizers was discussed in detail. Based on the limitations of existing research, further investigation in this area is expected to provide valuable insights for the development and practical implementation of technologies aimed at reducing soil microplastics and resistance genes.
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Affiliation(s)
- Tianhao Li
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Shiyu Tao
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Mengjie Ma
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Shiwei Liu
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China
| | - Maocai Shen
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China.
| | - Huijuan Zhang
- School of Energy and Environment, Anhui University of Technology, Maanshan, Anhui 243002, PR China.
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38
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Zhang R, Gong C, Li J, Zhuang H, Lan L, Zhou L, Shan S, Wang Y. Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169181. [PMID: 38072280 DOI: 10.1016/j.scitotenv.2023.169181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.
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Affiliation(s)
- Ranran Zhang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China.
| | - Chenpan Gong
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Jimin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China
| | - Haifeng Zhuang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Lihua Lan
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Liuyuan Zhou
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resource, Zhejiang University of Science and Technology, Zhejiang, Hangzhou 310023, China
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, 710129, China
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Corte Pause F, Urli S, Crociati M, Stradaioli G, Baufeld A. Connecting the Dots: Livestock Animals as Missing Links in the Chain of Microplastic Contamination and Human Health. Animals (Basel) 2024; 14:350. [PMID: 38275809 PMCID: PMC10812800 DOI: 10.3390/ani14020350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
Plastic pollution is a global diffuse threat, especially considering its fragmentation into microplastics (MPs) and nanoplastics (NPs). Since the contamination of the aquatic environment is already well studied, most studies have now focused on the soil. Moreover, the number of studies on the exposure routes and toxic effects of MNPs in humans is continuously increasing. Although MNPs can cause inflammation, cytotoxicity, genotoxicity and immune toxicity in livestock animals, which can accumulate ingested/inhaled plastic particles and transfer them to humans through the food chain, research on this topic is still lacking. In considering farm animals as the missing link between soil/plant contamination and human health effects, this paper aims to describe their importance as carriers and vectors of MNP contamination. As research on this topic is in its early stages, there is no standard method to quantify the amount and the characteristics of MNPs in different matrices. Therefore, the creation of a common database where researchers can report data on MNP characteristics and quantification methods could be helpful for both method standardization and the future training of an AI tool for predicting the most abundant/dangerous polymer(s), thus supporting policy decisions to reduce plastic pollution and perfectly fitting with One Health principles.
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Affiliation(s)
- Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Delle Scienze 206, 33100 Udine, Italy; (F.C.P.); (S.U.)
| | - Susy Urli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Delle Scienze 206, 33100 Udine, Italy; (F.C.P.); (S.U.)
| | - Martina Crociati
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo 4, 06126 Perugia, Italy;
- Centre for Perinatal and Reproductive Medicine, University of Perugia, 06129 Perugia, Italy
| | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via Delle Scienze 206, 33100 Udine, Italy; (F.C.P.); (S.U.)
| | - Anja Baufeld
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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Feng M, Liu Y, Yang L, Li Z. Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review. BIORESOURCE TECHNOLOGY 2023; 390:129861. [PMID: 37863331 DOI: 10.1016/j.biortech.2023.129861] [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: 07/16/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.
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Affiliation(s)
- Minmin Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Yuanwang Liu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China.
| | - Lie Yang
- Wuhan University of Technology, School of Resources & Environmental Engineering, Wuhan 430070, China
| | - Zhaojun Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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41
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Kenneth MJ, Koner S, Hsu GJ, Chen JS, Hsu BM. A review on the effects of discharging conventionally treated livestock waste to the environmental resistome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122643. [PMID: 37775024 DOI: 10.1016/j.envpol.2023.122643] [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: 06/09/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.
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Affiliation(s)
- Mutebi John Kenneth
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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42
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Liang C, Wei Y, Wang X, Gao J, Cui H, Zhang C, Liu J. Analysis of Resistance Gene Diversity in the Intestinal Microbiome of Broilers from Two Types of Broiler Farms in Hebei Province, China. Antibiotics (Basel) 2023; 12:1664. [PMID: 38136698 PMCID: PMC10741226 DOI: 10.3390/antibiotics12121664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
The crucial reservoir of antibiotic resistance genes (ARGs) within the chicken intestinal microbiome poses a serious threat to both animal and human health. In China, the overuse of antibiotics has significantly contributed to the proliferation of ARGs in the chicken intestinal microbiome, which is a serious concern. However, there has been relatively little research on the diversity of resistance genes in the chicken intestinal microbiome since the implementation of the National Pilot Work Program for Action to Reduce the Use of Veterinary Antimicrobial Drugs in China. The objective of this study was to analyze the diversity of antibiotic resistance genes carried by the chicken intestinal microbiome in both standard farms (SFs), which implement antibiotic reduction and passed national acceptance, and nonstandard farms (NSFs), which do not implement antibiotic reductions, in Hebei Province. Fresh fecal samples of broiler chickens were collected from SFs (n = 4) and NSF (n = 1) and analyzed using high-throughput qPCR technology. Our findings revealed that all five farms exhibited a wide range of highly abundant ARGs, with a total of 201 ARGs and 7 MGEs detected in all fecal samples. The dominant ARGs identified conferred resistance to aminoglycosides, macrolide-lincosamide-streptomycin B (MLSB), and tetracycline antibiotics. Cellular protection mechanisms were found to be the primary resistance mechanism for these ARGs. The analysis of the co-occurrence network demonstrated a significant positive correlation between the abundance of MGEs and ARGs. The SF samples showed a significantly lower relative abundance of certain ARGs than the NSF samples (p < 0.05). The results of this study show that the abundance of ARGs demonstrated a downward trend after the implementation of the National Pilot Work Program for Action to Reduce the Usage of Veterinary Antimicrobial Drugs in Hebei Province, China.
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Affiliation(s)
| | | | | | | | | | - Cheng Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China (J.G.)
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China (J.G.)
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43
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Yang H, Lu H, Li K, Huang Y, Li Q. Insights into antibiotic resistance gene abundances and regulatory mechanisms induced by ionic liquids during composting. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118652. [PMID: 37481880 DOI: 10.1016/j.jenvman.2023.118652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/15/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
This study investigated the regulatory mechanism of the evolution of antibiotic resistance genes (ARGs) during the composting process with sawdust and cow manure as raw materials using ionic liquids (ILs) pretreatment. The results showed that genes of MLS, chloramphenicol, tetracycline, beta - lactam as composting gradually decreased. From day0 to day3, MLS in control group (CK) and experimental group (T) decreased by 25.62% and 26.66%, respectively. Tetracycline decreased by 7.21% in CK and by 7.86% in T. Chloramphenicol decreased by 2.85% in CK and 3.34% in T. Beta-lactam decreased by 1.95% in Ck and by 3.69% in T. Mechanism studies have shown that ILs can effectively decompose extracellular polymeric substances (EPS) and enhance lactose dehydrogenase (LDH) release, resulting in ARGs release and elimination. Meanwhile, ILs pretreatment can inhibit growth of some ARGs hosts, especially Firmicutes, resulting in decreased ARGs. Moreover, metabolic pathways and related genes take part in ARGs transmission were down regulated, leading to decreased ARGs.
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Affiliation(s)
- Hongxiang Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Heng Lu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yite Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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44
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Zhu N, Long Y, Kan Z, Zhu Y, Jin H. Reduction of mobile genetic elements determines the removal of antibiotic resistance genes during pig manure composting after thermal pretreatment. BIORESOURCE TECHNOLOGY 2023; 387:129672. [PMID: 37586429 DOI: 10.1016/j.biortech.2023.129672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
Animal manure is a primary repository of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). This work explored the efficiency of ARGs and MGEs removal during pig manure composting after thermal pretreatment (TPC) and the underlying mechanisms. TPC resulted in a decrease of 94.7% and 92.3% in the relative abundance of ARGs and MGEs which was 48.9% and 76.6% lower than control, respectively. Network analysis indicated that reductions of ARGs and MGEs in TPC were relevant to decrease in the amount and abundance of bacterial hosts. Furthermore, total ARGs abundance in TPC was correlated with that of intI1 and Tn916/1545 (P < 0.001). Redundancy analysis supported a leading role of MGEs in ARGs dynamics in TPC. Reduction of MGEs rather than bacterial hosts contributed mainly to ARGs removal in TPC, as revealed by structural equation modeling. In conclusion, TPC was an effective method to treat animal manure containing ARGs.
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Affiliation(s)
- Ning Zhu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujiao Long
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zexin Kan
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanyun Zhu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongmei Jin
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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45
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Zhou Y, Kurade MB, Sirohi R, Zhang Z, Sindhu R, Binod P, Jeon BH, Syed A, Verma M, Awasthi MK. Biochar as functional amendment for antibiotic resistant microbial community survival during hen manure composting. BIORESOURCE TECHNOLOGY 2023; 385:129393. [PMID: 37364648 DOI: 10.1016/j.biortech.2023.129393] [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: 04/10/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
The study aim was to reveal the mechanism of impact of two type biochar on composting of hen manure (HM) and wheat straw (WS). Biochar derived from coconut shell and bamboo used as additives to reduce antibiotic resistant bacteria (ARB) in HM compost. The results manifested that effect of biochar amendment was significant to reduce ARB in HM composting. Compared with control, the microbial activity and abundance were increased in both biochar applied treatment, and bacterial community was changed. Additionally, network analysis revealed that biochar amendment increased the quantity of microorganisms related to organic matter degrading. Among them, coconut shell biochar (CSB) played a pioneering role to mitigate ARB to better exert its effects. Structural correlation analysis showed that CSB reduce ARB mobility and promote organic matter degradation via improving beneficial bacterial community structure. Overall, composting with participation of biochar amendment stimulated antibiotic resistance bacterial dynamics. These results evidence practical value for scientific research and lay the foundation for agricultural promotion of composting.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Mayur B Kurade
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Ranjna Sirohi
- School of Health Sciences and Technology, University of Petroleum and Energy Studies Dehradun, 248007 Uttarakhand, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 691505, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Meenakshi Verma
- University Centre for Research & Development, Department of Chemistry, Chandigarh University Gharuan, Mohali, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, 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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Abdugheni R, Li L, Yang ZN, Huang Y, Fang BZ, Shurigin V, Mohamad OAA, Liu YH, Li WJ. Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects. Microorganisms 2023; 11:1897. [PMID: 37630456 PMCID: PMC10456746 DOI: 10.3390/microorganisms11081897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.
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Affiliation(s)
- Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Ni Yang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yin Huang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Vyacheslav Shurigin
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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Fan Q, Zhang J, Shi H, Chang S, Hou F. Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting. Appl Environ Microbiol 2023; 89:e0064523. [PMID: 37409977 PMCID: PMC10370317 DOI: 10.1128/aem.00645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023] Open
Abstract
Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.
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Affiliation(s)
- Qingshan Fan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jing Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hairen Shi
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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49
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Zalewska M, Błażejewska A, Czapko A, Popowska M. Pig manure treatment strategies for mitigating the spread of antibiotic resistance. Sci Rep 2023; 13:11999. [PMID: 37491438 PMCID: PMC10368742 DOI: 10.1038/s41598-023-39204-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023] Open
Abstract
Due to the risk of pathogenic antibiotic-resistant bacteria and their antibiotic-resistance genes transfer from livestock feces to the soil and cultivated crops, it is imperative to find effective on-farm manure treatments to minimize that hazardous potential. An introduced worldwide policy of sustainable development, focus on ecological agricultural production, and the circular economy aimed at reducing the use of artificial fertilizers; therefore, such treatment methods should also maximize the fertilization value of animal manure. The two strategies for processing pig manure are proposed in this study-storage and composting. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, and in the resistome, compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harboring antibiotic resistance genes, including those responsible for multi-drug resistance. Overall, the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to crops and the food chain while providing essential fertilizer ingredients.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Czapko
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.
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Shoaib M, He Z, Geng X, Tang M, Hao R, Wang S, Shang R, Wang X, Zhang H, Pu W. The emergence of multi-drug resistant and virulence gene carrying Escherichia coli strains in the dairy environment: a rising threat to the environment, animal, and public health. Front Microbiol 2023; 14:1197579. [PMID: 37520353 PMCID: PMC10382034 DOI: 10.3389/fmicb.2023.1197579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/08/2023] [Indexed: 08/01/2023] Open
Abstract
Escherichia coli is a common inhabitant of the intestinal microbiota and is responsible for udder infection in dairy cattle and gastro-urinary tract infections in humans. We isolated E. coli strains from a dairy farm environment in Xinjiang, China, and investigated their epidemiological characteristics, phenotypic and genotypic resistance to antimicrobials, virulence-associated genes, and phylogenetic relationship. A total of 209 samples were collected from different sources (feces, slurry, water, milk, soil) and cultured on differential and selective agar media (MAC and EMB). The presumptive identification was done by the VITEK2 system and confirmed by 16S rRNA gene amplification by PCR. Antimicrobial susceptibility testing was done by micro-dilution assay, and genomic characterization was done by simple and multiplex polymerase chain reaction (PCR). A total of 338 E. coli strains were identified from 141/209 (67.5%) of the samples. Most of the E. coli strains were resistant to sulfamethoxazole/trimethoprim (62.43%), followed by cefotaxime (44.08%), ampicillin (33.73%), ciprofloxacin (31.36%), tetracycline (28.99%), and a lesser extent to florfenicol (7.99%), gentamicin (4.44%), amikacin (1.77%), and fosfomycin (1.18%). All of the strains were susceptible to meropenem, tigecycline, and colistin sulfate. Among the resistant strains, 44.4% were identified as multi-drug resistant (MDR) showing resistance to at least one antibiotic from ≥3 classes of antibiotics. Eighteen out of 20 antibiotic-resistance genes (ARGs) were detected with sul2 (67.3%), blaTEM (56.3%), gyrA (73.6%), tet(B) (70.4%), aph(3)-I (85.7%), floR (44.4%), and fosA3 (100%, 1/1) being the predominant genes among different classes of antibiotics. Among the virulence-associated genes (VAGs), ompA was the most prevalent (86.69%) followed by ibeB (85.0%), traT (84.91%), ompT (73.96%), fyuA (23.1%), iroN (23.1%), and irp2 gene (21.9%). Most of the E. coli strains were classified under phylogenetic group B1 (75.45%), followed by A (18.34%), C (2.96%), D (1.18%), E (1.18%), and F (0.30%). The present study identified MDR E. coli strains carrying widely distributed ARGs and VAGs from the dairy environment. The findings suggested that the dairy farm environment may serve as a source of mastitis-causing pathogens in animals and horizontal transfer of antibiotic resistance and virulence genes carrying bacterial strains to humans via contaminated milk and meat, surface water and agricultural crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
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