1
|
Fu Y, Jia F, Su J, Xu X, Zhang Y, Li X, Jiang X, Schäffer A, Virta M, Tiedje JM, Wang F. Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134252. [PMID: 38657507 DOI: 10.1016/j.jhazmat.2024.134252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.
Collapse
Affiliation(s)
- Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feiran Jia
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Jingfang Su
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xinyao Xu
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Yuqin Zhang
- University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Xiangzhen Li
- Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andreas Schäffer
- Institute for Environmental Research, RWTH Aachen University, Aachen 52074, Germany
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Environmental Research, RWTH Aachen University, Aachen 52074, Germany.
| |
Collapse
|
2
|
Bünemann EK, Reimer M, Smolders E, Smith SR, Bigalke M, Palmqvist A, Brandt KK, Möller K, Harder R, Hermann L, Speiser B, Oudshoorn F, Løes AK, Magid J. Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168901. [PMID: 38042198 DOI: 10.1016/j.scitotenv.2023.168901] [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: 07/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023]
Abstract
Use of nutrients recycled from societal waste streams in agriculture is part of the circular economy, and in line with organic farming principles. Nevertheless, diverse contaminants in waste streams create doubts among organic farmers about potential risks for soil health. Here, we gather the current knowledge on contaminant levels in waste streams and recycled nutrient sources, and discuss associated risks. For potentially toxic elements (PTEs), the input of zinc (Zn) and copper (Cu) from mineral feed supplements remains of concern, while concentrations of PTEs in many waste streams have decreased substantially in Europe. The same applies to organic contaminants, although new chemical groups such as flame retardants are of emerging concern and globally contamination levels differ strongly. Compared to inorganic fertilizers, application of organic fertilizers derived from human or animal feces is associated with an increased risk for environmental dissemination of antibiotic resistance. The risk depends on the quality of the organic fertilizers, which varies between geographical regions, but farmland application of sewage sludge appears to be a safe practice as shown by some studies (e.g. from Sweden). Microplastic concentrations in agricultural soils show a wide spread and our understanding of its toxicity is limited, hampering a sound risk assessment. Methods for assessing public health risks for organic contaminants must include emerging contaminants and potential interactions of multiple compounds. Evidence from long-term field experiments suggests that soils may be more resilient and capable to degrade or stabilize pollutants than often assumed. In view of the need to source nutrients for expanding areas under organic farming, we discuss inputs originating from conventional farms vs. non-agricultural (i.e. societal) inputs. Closing nutrient cycles between agriculture and society is feasible in many cases, without being compromised by contaminants, and should be enhanced, aided by improved source control, waste treatment and sound risk assessments.
Collapse
Affiliation(s)
- E K Bünemann
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070 Frick, Switzerland.
| | - M Reimer
- University of Hohenheim, Department of Fertilization and Soil Matter Dynamics, Fruwirthstr. 20, 70599 Stuttgart, Germany; Aarhus University, Department of Agroecology, Blichers Allé 20, 8830 Tjele, Denmark
| | - E Smolders
- Division Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - S R Smith
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - M Bigalke
- Department of Soil Mineralogy and Soil Chemistry, Institute for Applied Geosciences, Technical University of Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
| | - A Palmqvist
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - K K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - K Möller
- University of Hohenheim, Department of Fertilization and Soil Matter Dynamics, Fruwirthstr. 20, 70599 Stuttgart, Germany
| | - R Harder
- Environmental Engineering Group, Department of Energy and Technology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - L Hermann
- Proman Management GmbH, Weingartenstrasse 92, 2214 Auersthal, Austria
| | - B Speiser
- Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070 Frick, Switzerland
| | - F Oudshoorn
- Innovation Centre for Organic Farming (ICOEL), Agro Food Park 26, 8200 Aarhus, Denmark
| | - A K Løes
- Norwegian Centre for Organic Agriculture (NORSØK), Gunnars veg 6, N-6630 Tingvoll, Norway
| | - J Magid
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| |
Collapse
|
3
|
Shan X, Liu C, Song L, Huan H, Chen H. Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122575. [PMID: 37742860 DOI: 10.1016/j.envpol.2023.122575] [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: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023]
Abstract
Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.
Collapse
Affiliation(s)
- Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Huan Huan
- Technical Centre for Soil, Agricultural and Rural Ecology and Environment, Ministry of Ecology and Environment of the People's Republic of China, Beijing, 100012, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
| |
Collapse
|
4
|
Tang Q, Sui Q, Wei Y, Shen P, Zhang J. Swine-manure composts induce the enrichment of antibiotic-resistant bacteria but not antibiotic resistance genes in soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118707. [PMID: 37536132 DOI: 10.1016/j.jenvman.2023.118707] [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: 04/07/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
Composting is a common and effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from animal manure. However, it is unclear whether the advantages of composting for the control of ARGs and ARB can be further increased in land application. This study investigated the fate of ARB and ARGs after land application of swine-manure composts (SMCs) to three different soil types (red soil, loess and black soil). The results showed that although the SMCs caused an increase in the abundance of total ARGs in the soil in the short period, they significantly reduced (p < 0.01) the abundance of total ARGs after 82 days compared to the control. The decay rate of ARGs reflected by the half-life times (t1/2) varied by soil type, with red soil being the longest. The SMCs mainly introduced ermF, tetG and tetX into the soils, while these ARGs quickly declined to the control level. Notably, SMCs increased the number of ARB in the soils, especially for cefotaxime-resistant bacteria. Although SMCs only affected the microbiome significantly during the early stage (p < 0.05), it took a much longer time for the microbiome to recover compared to the control. Statistical analysis indicated that changes in the microbial community contributed more to the fate of ARGs during SMCs land application than other factors. Overall, it is proposed that the advantages of ARGs control in the composting process for swine manure can be further increased in land application, but it can still bring some risks in regard to ARB.
Collapse
Affiliation(s)
- Qihe Tang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Life Science and Technology, Guangxi University, Nanning, 530005, China
| | - Qianwen Sui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peihong Shen
- College of Life Science and Technology, Guangxi University, Nanning, 530005, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
5
|
Mei Z, Fu Y, Wang F, Xiang L, Hu F, Harindintwali JD, Wang M, Virta M, Hashsham SA, Jiang X, Tiedje JM. Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132388. [PMID: 37639796 DOI: 10.1016/j.jhazmat.2023.132388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.
Collapse
Affiliation(s)
- Zhi Mei
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Yuhao Fu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Leilei Xiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Hu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyi Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Geographical Sciences, Nantong University, Nantong 226001, China
| | - Marko Virta
- Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Syed A Hashsham
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Liu Y, Feng M, Johansen A, Cheng D, Xue J, Feng Y, Fan S, Li Z. Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161785. [PMID: 36736399 DOI: 10.1016/j.scitotenv.2023.161785] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.
Collapse
Affiliation(s)
- Yuanwang Liu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Minmin Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Anders Johansen
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, Roskilde 4000, Denmark
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Scion, Private Bag 29237, Christchurch 8440, New Zealand
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuanghu Fan
- College of Life Science, Langfang Normal University, Langfang 065000, China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
8
|
Han B, Shen S, Yang F, Wang X, Gao W, Zhang K. Exploring antibiotic resistance load in paddy-upland rotation fields amended with commercial organic and chemical/slow release fertilizer. Front Microbiol 2023; 14:1184238. [PMID: 37125153 PMCID: PMC10140351 DOI: 10.3389/fmicb.2023.1184238] [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: 03/11/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Agricultural fertilization caused the dissemination of antibiotic resistance genes (ARGs) in agro-ecological environment, which poses a global threat to crop-food safety and human health. However, few studies are known about the influence of different agricultural fertilization modes on antibiotic resistome in the paddy-upland rotation soils. Therefore, we conducted a field experiment to compare the effect of different fertilization (chemical fertilizer, slow release fertilizer and commercial organic fertilizer replacement at various rates) on soil antibiotic resistome in paddy-upland rotation fields. Results revealed that a total of 100 ARG subtypes and 9 mobile genetic elements (MGEs) occurred in paddy-upland rotation soil, among which MDR-ARGs, MLSB-ARGs and tet-ARGs were the dominant resistance determinants. Long-term agricultural fertilization remarkably facilitated the vertical accumulation of ARGs, in particular that bla ampC and tetO in relative abundance showed significant enrichment with increasing depth. It's worth noting that slow release fertilizer significantly increased soil ARGs, when comparable to manure with 20% replacing amount, but chemical fertilizer had only slight impact on soil ARGs. Fertilization modes affected soil microbial communities, mainly concentrated in the surface layer, while the proportion of Proteobacteria with the highest abundance decreased gradually with increasing depth. Furthermore, microbial community and MGEs were further proved to be essential factors in regulating the variability of ARGs of different fertilization modes by structural equation model, and had strong direct influence (λ = 0.61, p < 0.05; λ = 0. 55, p < 0.01). The results provided scientific guidance for reducing the spreading risk of ARGs and control ARG dissemination in agricultural fertilization.
Collapse
Affiliation(s)
- Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
- Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
- Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China
- *Correspondence: Fengxia Yang,
| | - Xiaolong Wang
- School of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Wenxuan Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
- Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, Dali, China
- Keqiang Zhang,
| |
Collapse
|
9
|
Zhang H, Ling H, Zhou R, Tang J, Hua R, Wu X. Contrasting dynamics of manure-borne antibiotic resistance genes in different soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114162. [PMID: 36252512 DOI: 10.1016/j.ecoenv.2022.114162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance genes (ARGs) are important biological contamination factors in soil systems, posing direct or indirect threats to soil health, food safety and human health. The ubiquitous pollution of ARGs is usually implicated with the application of organic manures in agricultural soil ecosystem. However, little is known about the transmission and fate of ARGs after manure input concerning different soils. Herein, the transmission potential and temporal dynamics of manure-associated ARGs was characterized with three different agricultural soils collected from Jiangxi (JX), Zhejiang (ZJ), and Jilin (JL), respectively. The results show that manure input did not affect the total abundance of ARGs in the receiving soils, but remarkedly alter the compositions of ARGs in soils. The manure-associated ARGs were significantly enriched in the manure-amended soils, including genes conferring resistance to sulfonamide, aminoglycoside, tetracycline, chloramphenicol, and trimethoprim with the fold of 1.97 - 27.86. Variance partitioning analysis showed that the major variances of ARG community was explained by mobile genetic elements and bacterial profile (> 76%) but not the concentrations of heavy metals and antibiotics. Furthermore, 31, 37, and 38 ARG subtypes were identified as the potential extrinsic ARGs derived from manures in the JX, ZJ, and JL soils, respectively, including 13 shared ARG subtypes. It was also found that the manure-associated ARGs (aadA, sul1, sul2, tetC, and tetG) declined with the incubation time in the JX and ZJ soils, whereas they firstly decreased and then increased in the JL soil. The abundance of these five ARGs in the JL soil was significantly higher than that in the JX and ZJ soils. Collectively, this finding revealed that soil type was responsible for the transmission and fate of manure-associated ARGs in agroecosystem.
Collapse
Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Hong Ling
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Ruofei Zhou
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China.
| |
Collapse
|
10
|
Flores-Orozco D, Levin D, Kumar A, Sparling R, Cicek N. A meta-analysis reveals that operational parameters influence levels of antibiotic resistance genes during anaerobic digestion of animal manures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152711. [PMID: 34974005 DOI: 10.1016/j.scitotenv.2021.152711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion (AD) has shown the potential to reduce the numbers and types of antibiotic-resistance genes (ARG) present in animal manures. However, the variability of the results has limited the ability to draw solid conclusions. To address this issue, we performed a series of meta-analyses to evaluate how AD of pig, cattle, and dairy manures affects ARG levels and how different parameters, such as temperature, pH, digestion times, and the addition of other substances (e.g., solids, antibiotics) influence ARG changes. Twenty studies with enough details on changes in ARG levels during the AD process were identified and used for the meta-analyses. The results suggested that AD could significantly reduce ARG levels regardless of the conditions of the process. Also, thermophilic AD was more effective than mesophilic AD at reducing ARGs, although this difference was only significant for pig manures. The results also suggested that long digestion times (>50 days) yielded better ARG reduction rates, and that the addition of solids from an external source (co-digestion) negatively affected the efficiency of ARG reduction. In general, the results suggested that ARG changes during AD could be linked to the abundance and activity of hydrolytic communities.
Collapse
Affiliation(s)
- Daniel Flores-Orozco
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - David Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nazim Cicek
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada
| |
Collapse
|
11
|
Fu Y, Wang F, Wang Z, Mei Z, Jiang X, Schäffer A, Virta M, Tiedje JM. Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:151386. [PMID: 34742956 DOI: 10.1016/j.scitotenv.2021.151386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.
Collapse
Affiliation(s)
- Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Andreas Schäffer
- RWTH Aachen University, Institute for Environmental Research, Aachen 52074, Germany
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| |
Collapse
|
12
|
Liu Y, Cheng D, Xue J, Feng Y, Wakelin SA, Weaver L, Shehata E, Li Z. Fate of bacterial community, antibiotic resistance genes and gentamicin residues in soil after three-year amendment using gentamicin fermentation waste. CHEMOSPHERE 2022; 291:132734. [PMID: 34743798 DOI: 10.1016/j.chemosphere.2021.132734] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 05/20/2023]
Abstract
Over a three-year field trial, the impacts of composted and raw gentamicin fermentation waste (GFW) application to land on residual soil gentamicin levels, physicochemical properties, bacterial community composition, and antibiotic resistance genes (ARGs) were assessed. In the saline-alkali soil tested, GFW application decreased electrical conductivity (EC) and pH. Importantly, there was no measurable long-term accumulation of gentamicin as a result of GFW addition. Changes in the abundance of Bacillus was primarily associated with degradation of gentamicin in soil, whereas wider (i.e. more general) shifts in bacterial communities over the treatments was linked to alteration of soil physicochemical properties, particularly pH, total nitrogen, dissolved organic carbon, EC, NO3--N and NH4+-N. Compared with other treatments, soils receiving composted GFW harbored more types of ARGs and significantly higher (P < 0.05) abundances of mobile genes elements (MGEs) (especially IncQ and Int1) and aminoglycoside ARGs (especially aminoglycoside phosphotransferases genes, APH). Finally, the abundances of ARGs in soils receiving raw and composted GFW were 59.60% and 50.26% higher than that in soils only receiving chemical fertilizer, respectively. Specifically, the abundances of APH, especially strB, were significantly higher than other kinds of ARGs (P < 0.05). The results of linear regression and partial least squares path model showed that MGEs, including plasmids, integrons, and transposons, along with soil properties (EC and NH4+-N) were the main factors associated with change in ARGs. Furthermore, different MGEs were involved in different transfer mechanisms of specific ARGs. Our findings demonstrated the potential risks of using raw and composted GFW as fertilizer, and suggest potential solutions to this problem.
Collapse
Affiliation(s)
- Yuanwang Liu
- Hebei Key Laboratory of Applied Chemistry, Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, 066004, PR China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; Scion, Private Bag, 29237, Christchurch, New Zealand
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | | | - Louise Weaver
- Institute of Environmental Science and Research Ltd, Christchurch, 8041, New Zealand
| | - Ebrahim Shehata
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; Institute of Animal science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China.
| |
Collapse
|
13
|
Fu Y, Jia M, Wang F, Wang Z, Mei Z, Bian Y, Jiang X, Virta M, Tiedje JM. Strategy for Mitigating Antibiotic Resistance by Biochar and Hyperaccumulators in Cadmium and Oxytetracycline Co-contaminated Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16369-16378. [PMID: 34695355 DOI: 10.1021/acs.est.1c03434] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global prevalence of antibiotic resistance genes (ARGs) is of increasing concern as a serious threat to ecological security and human health. Irrigation with sewage and farmland application of manure or biosolids in agricultural practices introduce substantial selective agents such as antibiotics and toxic metals, aggravating the transfer of ARGs from the soil environment to humans via the food chain. To address this issue, a hyperaccumulator (Sedum plumbizincicola) combined with biochar amendment was first used to investigate the mitigation of the prevalence of ARGs in cadmium and oxytetracycline co-contaminated soil by conducting a pot experiment. The addition of biochar affected the distribution of ARGs in soil and plants differently by enhancing their prevalence in the soil but restraining transmission from the soil to S. plumbizincicola. The planting of S. plumbizincicola resulted in an increase in ARGs in the soil environment. A structural equation model illustrated that mobile genetic elements played a dominant role in shaping the profile of ARGs. Taken together, these findings provide a practical understanding for mitigating the prevalence of ARGs in this soil system with complex contamination and can have profound significance for agricultural management in regard to ARG dissemination control.
Collapse
Affiliation(s)
- Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyun Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210008, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
14
|
Wang Q, Guo S, Hou Z, Lin H, Liang H, Wang L, Luo Y, Ren H. Rainfall facilitates the transmission and proliferation of antibiotic resistance genes from ambient air to soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149260. [PMID: 34352459 DOI: 10.1016/j.scitotenv.2021.149260] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is common in bacterial communities and appears to be correlated with human activities. However, the source of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in remote regions remains unclear. In this study, we examined the abundance of ARGs in fine particulate matter (PM2.5) as a carrier throughout the rainfall process (4 mm rain/h) to observe the effects of rainfall on the transmission of ARGs. The results suggested that rainwater served as a reservoir that facilitated the spread of ARGs and that wind and particulate matter (PM) concentrations might be meteorological parameters that influence the distribution of ARGs in rainwater. In addition, soil microcosm experiments were performed to investigate the influence of rainfall on antibiotic resistance in soils with different environmental backgrounds. Rainwater facilitated the proliferation of ARGs and mobile genetic elements (MGEs) from ambient air to soil, and this influence was more obvious in heavy metal-contaminated soil. This is the first study to investigate the routes by which rainfall acts as a mobile reservoir to facilitate the transmission and proliferation of ARGs, and the results indicate the potential source of ARGs in remote regions where humans rarely interfere.
Collapse
Affiliation(s)
- Qing Wang
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei University of Engineering, Handan 056038, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Shaoyue Guo
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei University of Engineering, Handan 056038, China
| | - Zelin Hou
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei University of Engineering, Handan 056038, China
| | - Huai Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Haiyin Liang
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei University of Engineering, Handan 056038, China
| | - Litao Wang
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei University of Engineering, Handan 056038, China
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| |
Collapse
|
15
|
Mei Z, Xiang L, Wang F, Xu M, Fu Y, Wang Z, Hashsham SA, Jiang X, Tiedje JM. Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment. ENVIRONMENT INTERNATIONAL 2021; 157:106830. [PMID: 34418848 DOI: 10.1016/j.envint.2021.106830] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 05/23/2023]
Abstract
The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 104 and 1.1 × 106 in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 107 and 3.2 × 107 of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.
Collapse
Affiliation(s)
- Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leilei Xiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhao Fu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| |
Collapse
|
16
|
Finn DR, Maldonado J, de Martini F, Yu J, Penton CR, Fontenele RS, Schmidlin K, Kraberger S, Varsani A, Gile GH, Barker B, Kollath DR, Muenich RL, Herckes P, Fraser M, Garcia-Pichel F. Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149239. [PMID: 34325138 DOI: 10.1016/j.scitotenv.2021.149239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Air carries a diverse load of particulate microscopic biological matter in suspension, either aerosolized or aggregated with dust particles, the aerobiome, which is dispersed by winds from sources to sinks. The aerobiome is known to contain microbes, including pathogens, as well as debris or small-sized propagules from plants and animals, but its variability and composition has not been studied comprehensibly. To gain a dynamic insight into the aerobiome existing over a mixed-use dryland setting, we conducted a biologically comprehensive, year-long survey of its composition and dynamics for particles less than 10 μm in diameter based on quantitative analyses of DNA content coupled to genomic sequencing. Airborne biological loads were more dependent on seasonal events than on meteorological conditions and only weakly correlated with dust loads. Core aerobiome species could be understood as a mixture of high elevation (e.g. Microbacteriaceae, Micrococcaceae, Deinococci), and local plant and soil sources (e.g. Sphingomonas, Streptomyces, Acinetobacter). Despite the mixed used of the land surrounding the sampling site, taxa that contributed to high load events were largely traceable to proximal agricultural practices like cotton and livestock farming. This included not only the predominance of specific crop plant signals over those of native vegetation, but also that of their pathogens (bacterial, viral and eukaryotic). Faecal bacterial loads were also seasonally important, possibly sourced in intensive animal husbandry or manure fertilization activity, and this microbial load was enriched in tetracycline resistance genes. The presence of the native opportunistic pathogen, Coccidioides spp., by contrast, was detected only with highly sensitive techniques, and only rarely. We conclude that agricultural activity exerts a much stronger influence that the native vegetation as a mass loss factor to the land system and as an input to dryland aerobiomes, including in the dispersal of plant, animal and human pathogens and their genetic resistance characteristics.
Collapse
Affiliation(s)
- Damien R Finn
- Thünen Institut für Biodiversität, Johann Heinrich von Thünen Institut, Braunschweig 38116, Germany; The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Juan Maldonado
- Knowledge Enterprise Genomics Core, Arizona State University, Tempe 85287-5001, AZ, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Francesca de Martini
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Julian Yu
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - C Ryan Penton
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Kara Schmidlin
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Simona Kraberger
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA; Center for Evolution and Medicine, Arizona State University, Tempe 85287-5001, AZ, USA
| | - Gillian H Gile
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Bridget Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff 86011-4073, AZ, USA
| | - Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff 86011-4073, AZ, USA
| | - Rebecca L Muenich
- School of Sustainable Engineering, Arizona State University, Tempe 85287-3005, AZ, USA
| | - Pierre Herckes
- School of Molecular Sciences, Arizona State University, Tempe 85287-1604, AZ, USA
| | - Matthew Fraser
- School of Sustainable Engineering, Arizona State University, Tempe 85287-3005, AZ, USA
| | - Ferran Garcia-Pichel
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe 85287-5001, AZ, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| |
Collapse
|
17
|
Liu B, Yu K, Ahmed I, Gin K, Xi B, Wei Z, He Y, Zhang B. Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148372. [PMID: 34139488 DOI: 10.1016/j.scitotenv.2021.148372] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.
Collapse
Affiliation(s)
- Botao Liu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Imtiaz Ahmed
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Gin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
18
|
He LY, He LK, Gao FZ, Wu DL, Zou HY, Bai H, Zhang M, Ying GG. Dissipation of antibiotic resistance genes in manure-amended agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147582. [PMID: 33992936 DOI: 10.1016/j.scitotenv.2021.147582] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/25/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Soil antibiotic resistance due to animal manure application is of great concern in recent years. Little is known about the fate of antibiotic resistance genes (ARGs) in agricultural soils associated with long-term manure application. Here we used soil microcosms to investigate the dissipation of ARGs and the change of bacterial community in agricultural soil originated from a vegetable field which had received 24 years' swine manure application. Soil microcosms were conducted at different soil moistures and with or without biochar over a testing period of two years in lab. Results showed that continuous manure application induced an accumulation of ARGs in soil, wherein the dissipation of ARGs differed from those in non-manure amended soil. ARGs persisted in soils at least two years, although their abundance declined gradually. Meanwhile, soil moisture and biochar had significant impact on the fate of ARGs. ARGs dissipated faster in soil with higher moisture. Biochar amendment contributed to the maintenance of bacterial diversity. Within the two years of simulation experiment, biochar enhanced soil ARG retention as they dissipated slowly in the soil amended with biochar. Succession of microbial community may have sustained the transfer and resilience of ARGs. This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil.
Collapse
Affiliation(s)
- Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Lun-Kai He
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China.
| |
Collapse
|
19
|
Xue J, Wu J, Hu Y, Sha C, Yao S, Li P, Lin K, Cui C. Occurrence of heavy metals, antibiotics, and antibiotic resistance genes in different kinds of land-applied manure in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:40011-40021. [PMID: 33768462 DOI: 10.1007/s11356-021-13307-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Various pollutants remaining in the livestock and poultry manures pose potential threat to the soil ecosystem during land application, whose impact should be appreciated. The occurrence of heavy metals, antibiotics, and antibiotic resistance genes (ARGs) in swine manure (SM), chicken manure (CM), and the SM organic fertilizer (OF) were investigated. The order of total concentrations of antibiotics detected in manures was as follows: SM > CM > OF. The amount of ciprofloxacin (CIP) in SM reached up to 6.61 mg/kg, which only occupied 1% of the antibiotic concentration reported in the past years. The total concentration of thirteen ARGs in CM ranked first, reaching 7.35 × 1011 copies/g, among which the strB gene was detected with the highest concentration. It was worth noting that the qnr ARGs were persistent in OF with the absence of corresponding antibiotics, indicating ARGs were harder to remove than antibiotics during manure composting. Zn and Cu (46.5-843 mg/kg) were obviously higher than other seven heavy metals, and significantly correlated with most ARGs (p < 0.01). This study provided the basic data of the pollution in animal manures that will be land-applied, illuminating the original source of potential risk in soil ecosystem.
Collapse
Affiliation(s)
- Jiajia Xue
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, 508 Qinzhou Road, Shanghai, 200233, China.
| | - Yaru Hu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chenyan Sha
- Shanghai Academy of Environmental Sciences, 508 Qinzhou Road, Shanghai, 200233, China
| | - Shijie Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Peng Li
- College of Environmental Science and Engineering, Donghua University, 2999 Renmin North Road, Shanghai, 201600, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| |
Collapse
|
20
|
Wind L, Keenum I, Gupta S, Ray P, Knowlton K, Ponder M, Hession WC, Pruden A, Krometis LA. Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale. Front Microbiol 2021; 12:683410. [PMID: 34305845 PMCID: PMC8299786 DOI: 10.3389/fmicb.2021.683410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/07/2021] [Indexed: 02/01/2023] Open
Abstract
An integrated understanding of factors influencing the occurrence, distribution, and fate of antibiotic resistance genes (ARGs) in vegetable production systems is needed to inform the design and development of strategies for mitigating the potential for antibiotic resistance propagation in the food chain. The goal of the present study was to holistically track antibiotic resistance and associated microbiomes at three distinct pre-harvest control points in an agroecosystem in order to identify the potential impacts of key agricultural management strategies. Samples were collected over the course of a single growing season (67 days) from field-scale plots amended with various organic and inorganic amendments at agronomic rates. Dairy-derived manure and compost amendment samples (n = 14), soil samples (n = 27), and lettuce samples (n = 12) were analyzed via shotgun metagenomics to assess multiple pre-harvest factors as hypothetical control points that shape lettuce resistomes. Pre-harvest factors of interest included manure collection during/post antibiotic use, manure composting, and soil amended with organic (stockpiled manure/compost) versus chemical fertilizer. Microbial community resistome and taxonomic compositions were unique from amendment to soil to lettuce surface according to dissimilarity analysis. The highest resistome alpha diversity (i.e., unique ARGs, n = 642) was detected in amendment samples prior to soil application, while the composted manure had the lowest total ARG relative abundance (i.e., 16S rRNA gene-normalized). Regardless of amendment type, soils acted as an apparent ecological buffer, i.e., soil resistome and taxonomic profiles returned to background conditions 67 d-post amendment application. Effects of amendment conditions surprisingly re-emerged in lettuce phyllosphere resistomes, with the highest total ARG relative abundances recovered on the surface of lettuce plants grown in organically-fertilized soils (i.e., compost- and manure-amended soils). Co-occurrence analysis identified 55 unique ARGs found both in the soil amendments and on lettuce surfaces. Among these, arnA and pmrF were the most abundant ARGs co-occurring with mobile genetic elements (MGE). Other prominent ARG-MGE co-occurrences throughout this pre-harvest lettuce production chain included: TetM to transposon (Clostridiodies difficile) in the manure amendment and TriC to plasmid (Ralstonia solanacearum) on the lettuce surfaces. This suggests that, even with imposing manure management and post-amendment wait periods in agricultural systems, ARGs originating from manure can still be found on crop surfaces. This study demonstrates a comprehensive approach to identifying key control points for the propagation of ARGs in vegetable production systems, identifying potential ARG-MGE combinations that could inform future surveillance. The findings suggest that additional pre-harvest and potentially post-harvest interventions may be warranted to minimize risk of propagating antibiotic resistance in the food chain.
Collapse
Affiliation(s)
- Lauren Wind
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Partha Ray
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, United States.,Department of Animal Sciences, University of Reading, Reading, United Kingdom
| | - Katharine Knowlton
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, United States
| | - Monica Ponder
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Leigh-Anne Krometis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|
21
|
Lin ZJ, Zhou ZC, Zhu L, Meng LX, Shuai XY, Sun YJ, Chen H. Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144814. [PMID: 33540158 DOI: 10.1016/j.scitotenv.2020.144814] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Wastewater treatment plants (WWTPs) in China have been upgraded or renovated with a variety of emerging processes, but a comprehensive understanding of the behavior of antibiotic resistance genes (ARGs) in these WWTPs is still lacking. Here, the distribution of ARGs and bacterial community were investigated in a wastewater treatment plant with upgrading processes (WWTP-UP). 238 unique ARGs were detected in all samples. During the study period, the average ARGs concentration decreased by 98.4% along the entire treatment process. The removal efficiency of A2/O-membrane bioreactor (MBR) process was significantly higher than that of A2/O-high efficiency flocculent settling/cloth media filter (HEFS/CMF) process (p < 0.05), which corresponded to 3.5 and 2.1 log values on average, respectively. Notably, 35 ARGs and 14 mobile genetic elements (MGEs) were persistent in all samples. Based on the co-occurrence pattern revealed by network analysis, persistent ARGs possibly spread through the transfer of persistent MGEs among persistent bacteria. Using multiple linear regression analysis, we obtained 3 to 5 possible indicators for major ARG types, which might be served to evaluate the general distribution of ARGs or even predict the abundance of different ARG types. Our findings provide new insights into the impacts of upgrading process on ARGs and highlight the need for better strategies to improve ARGs elimination in WWTPs.
Collapse
Affiliation(s)
- Ze-Jun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Chao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Zhu
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ling-Xuan Meng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-Yi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu-Jie Sun
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
22
|
Cheng J, Tang X, Liu C. Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29241-29252. [PMID: 33555470 DOI: 10.1007/s11356-021-12746-8] [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: 10/02/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The increasing emergence of antibiotic-resistant genes (ARGs) represents a global threat to human health. Land application of animal manure is known to contribute considerably to the propagation and dispersal of antibiotic resistance in agro-ecosystems. Yet, the primary determinants of the fate of the soil resistome remain obscure. In this study, a pot experiment was conducted to examine temporal changes in ARGs, mobile genetic elements (MGEs), and bacterial communities in a weakly developed loamy soil (an entisol known as calcareous purple soil) upon addition of pig or chicken manure. On the day of manure application, substantial increases in the diversity and relative abundance of ARGs were observed in soil amended with raw pig manure. At the same time, no obvious changes were observed for soil amended with chicken manure. Antibiotic resistance in pig manure-amended soils rapidly decreased over time to a level that was still higher than that of unamended soil at 100 days after manure application. The results of the Mantel test and Procrustes analysis indicated that ARG profiles in soil were significantly correlated with the structure of the bacterial phylogeny. Variation partitioning analysis further revealed that the bacterial community played a major role in regulating the temporal changes in ARGs in soil following manure application. Increased numbers and relative abundances of MGEs and their significant positive correlations with ARGs were observed, which suggest that a potential contribution from lateral gene transfer to the persistence and spread of ARGs should not be overlooked. Overall, our findings provide a better understanding of the mechanisms underlying the dynamics of ARGs in entisols following manure application and have practical implications for managing manure applications in entisols of the study area and other areas.
Collapse
Affiliation(s)
- Jianhua Cheng
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangyu Tang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Chen Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| |
Collapse
|
23
|
Wind L, Krometis LA, Hession WC, Pruden A. Cross-comparison of methods for quantifying antibiotic resistance in agricultural soils amended with dairy manure and compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144321. [PMID: 33477102 DOI: 10.1016/j.scitotenv.2020.144321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Agricultural soils are often amended with livestock manure, making them a key reservoir of antibiotic resistance genes (ARGs). Given that soils are among the most microbially-diverse environments on the planet; effective characterization and quantification of the effects of manure-derived amendments on soil resistomes is a major challenge. This study examined the effects of dairy manure-derived amendments on agricultural soils via two strategies: quantification of anthropogenic ARG markers via qPCR and shotgun metagenomic resistome profiling; and these strategies were compared to a previously published antibiotic resistant fecal coliform dataset. Soil samples were collected throughout a 120 day complete block field experiment to compare the effects of amendment type on antibiotic resistance. Results of all three measurements were consistent with the hypothesis that the application of composted manure reduced antibiotic resistance in soil relative to the application of raw manure, although some differences were noted in comparing the patterns of the three measurements with time. Raw dairy manure-amended soils yielded high sul1 and tet(W) relative abundances on Day 0 (following amendment application), but significantly decreased to background levels by Day 67 (harvest) and Day 120 (study completion). Shotgun metagenomics similarly detected a decrease in the relative abundances of sulfonamide and tetracycline-associated ARGs over time in the raw manure- and compost-amended soils; however, these levels were significantly lower than those estimated by qPCR. Interestingly, although patterns of sulfonamide and tetracycline resistance among culturable fecal coliforms echoed those observed via qPCR and metagenomics; erythromycin resistant coliforms were directly recovered by culture in amended soils, but corresponding ARGs were not detected by qPCR or metagenomics. This study supports both composting and time restrictions as means of reducing the potential for antibiotic resistance in manure to spread via soil application. Results suggest some differences in finer conclusions drawn depending on which antibiotic resistance monitoring target is selected.
Collapse
Affiliation(s)
- Lauren Wind
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA.
| | - Leigh-Anne Krometis
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, 1145 Perry St, Durham Hall RM 403, Blacksburg, VA 24061, USA
| |
Collapse
|
24
|
Xu M, Wang F, Sheng H, Stedtfeld RD, Li Z, Hashsham SA, Jiang X, Tiedje JM. Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143737. [PMID: 33243511 DOI: 10.1016/j.scitotenv.2020.143737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.
Collapse
Affiliation(s)
- Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA.
| | - Hongjie Sheng
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Zhongpei Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| |
Collapse
|
25
|
Liu N, Xu L, Han L, Huang G, Ciric L. Microbiological safety and antibiotic resistance risks at a sustainable farm under large-scale open-air composting and composting toilet systems. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123391. [PMID: 32653795 DOI: 10.1016/j.jhazmat.2020.123391] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/10/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
This study evaluated the microbial safety and antibiotic resistance risks of a sustainable ecological farm under large-scale open-air composting (OC) and green composting toilet systems (CT). Samples of livestock manure, compost, soil, vegetables, and rainwater were analysed to determine the best treatment of wastes and risk assessment of land application. Results showed that pathogenic bacteria (PB) in livestock manure was significantly greater than that in the surrounding topsoil, while the distribution of bacteria resistant to amoxicillin (AMX), tetracycline (TC), and amoxicillin-tetracycline (AMX- TC) was the opposite through long-term resistance selection pressure. E. coli and Enterococcus were the dominant pathogens in feces and surrounding soil, respectively, and AMX-resistant bacteria dominated soil, compost, and vegetable samples. Overall, while OC may significantly increase antibiotic resistance and effectively remove fecal PB, CT offers faster consumption with greater antibiotic resistant bacteria (ARB) removal but more PB. Moreover, PB and ARB were concentrated in mature compost, soil in planting areas, vegetables, and rainwater. In farm soil and vegetables, AMX-resistant and AMX-TC-resistant bacterial communities displayed similar composition. These findings may explain the main pathways of PB transmission, migration and accumulation of ARB in farms, and the potential risks to human health through the food chain.
Collapse
Affiliation(s)
- Ning Liu
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Like Xu
- Healthy Infrastructure Research Group, Department of Civil, Environmental & Geomatic Engineering, University College London, Gower Street, WC1E 6BT London, UK
| | - Lujia Han
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Guangqun Huang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
| | - Lena Ciric
- Healthy Infrastructure Research Group, Department of Civil, Environmental & Geomatic Engineering, University College London, Gower Street, WC1E 6BT London, UK.
| |
Collapse
|
26
|
Flores-Orozco D, Patidar R, Levin DB, Sparling R, Kumar A, Çiçek N. Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure. BIORESOURCE TECHNOLOGY 2020; 315:123889. [PMID: 32717520 DOI: 10.1016/j.biortech.2020.123889] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.
Collapse
Affiliation(s)
- Daniel Flores-Orozco
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Rakesh Patidar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Nazim Çiçek
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| |
Collapse
|
27
|
Wang Q, Liu L, Hou Z, Wang L, Ma D, Yang G, Guo S, Luo J, Qi L, Luo Y. Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137055. [PMID: 32065888 DOI: 10.1016/j.scitotenv.2020.137055] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/08/2020] [Accepted: 01/31/2020] [Indexed: 05/19/2023]
Abstract
Recent studies have consistently demonstrated increasing abundances of antibiotic resistance genes (ARGs) in the absence of antibiotic use. There is a large amount of quantitative data that has correlated the elevated ARGs levels with the concentrations of heavy metals in environments with anthropogenic impact. However, the mechanisms by which heavy metals facilitate the proliferation and horizontal gene transfer of ARGs among environmental bacteria were still unknown. This study validated effects of four typical heavy metals (Cu, Cd, Pb, Zn) on the plasmid RP4 mediated conjugative transfer of ARGs in freshwater microcosms. The results suggested that the typical heavy metals including Cu, Pb and Zn would promote conjugative transfer of the plasmid RP4, and Cu (5.0 μg/L) had the greatest ability to increase conjugative transfer by 16-fold higher than the control groups. In conjugative transfer microcosms, the species of each cultivable transconjugant were isolated, and their minimum inhibitory concentrations (MICs) were assessed via antibiotic susceptibility testing. The mechanism of the increased conjugative transfer of Cu was that Cu induced cell damage and the reduced conjugative transfer of Cd was that Cd increased the content of extracellular polymers substances (EPS). This study confirms that heavy metal Cu facilitates the conjugative transfer of environmental-mediated plasmid RP4 by cell damage effect, therefore accelerating the transmission and proliferation of ARGs.
Collapse
Affiliation(s)
- Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Lei Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zelin Hou
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Litao Wang
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Dan Ma
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Guang Yang
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Shaoyue Guo
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Jinghui Luo
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Liying Qi
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China.
| |
Collapse
|