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Cui E, Zhou Z, Cui B, Fan X, Ali Abid A, Chen T, Gao F, Du Z. Effects of nitrogen fertilization on the fate of high-risk antibiotic resistance genes in reclaimed water-irrigated soil and plants. ENVIRONMENT INTERNATIONAL 2024; 190:108834. [PMID: 38908278 DOI: 10.1016/j.envint.2024.108834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
High-risk antibiotic resistance genes (ARGs) in reclaimed water-irrigated soil pose a potential threat to ecosystem and human health. Inorganic fertilization - including with nitrogen, a key ingredient in agricultural production - may affect the ARG profile in soil. However, little is known about nitrogen fertilization's influence on ARGs profiles in the soil-plant system. This study investigated the effects of different nitrogen fertilizer types (CO(NH2)2, NO3--N (NaNO3) and NH4+-N (NH4HCO3)) and different nitrogen fertilizer application rates (low, medium, high) on the distribution of high-risk ARGs in reclaimed water-irrigated soil and plants using quantitative PCR, high-throughput sequencing and metagenomic sequencing. Soil microcosms results revealed that nitrogen fertilization significantly affected the pattern of high-risk ARGs in soil, and also affected high-risk ARGs abundance and transfer capacity in plants. Compared with nitrogen fertilizer application rate, nitrogen fertilizer types significantly contributed to enhancing the soil resistome, with the order of CO(NH2)2 > NO3--N ≈ NH4+-N. The medium application of NO3--N and NH4+-N significantly reduced high-risk ARGs abundance in the leaf endophyte. Bacterial community mainly drove the variation of ARGs in nitrogen-fertilized soil-plant system, and class I integron and metal resistance genes (MRGs) also had direct effects on these high-risk ARGs. A similar high-risk ARGs pattern was also found in field plot experiments, and several dangerous pathogens were observed as the main high-risk ARGs potential hosts in nitrogen-fertilized soil. Based on an economic assessment, application of NH4+-N (NH4HCO3) could reduce costs by $1,312.83 ha-1 compared with NO3--N (NaNO3). These results showed that the more important role of nitrogen type might be an effective and economical way to control high-risk ARGs spread in soil-plant system under reclaimed water irrigation.
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Affiliation(s)
- Erping Cui
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100000, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bingjian Cui
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
| | - Abbas Ali Abid
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Zhejiang University, Hangzhou 310058, China
| | - Taotao Chen
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100000, China
| | - Feng Gao
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Zhenjie Du
- Institute of Farmland Irrigation of Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
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Li WJ, Li HZ, Xu J, Gillings MR, Zhu YG. Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10796-10805. [PMID: 38853591 DOI: 10.1021/acs.est.4c02497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D2O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.
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Affiliation(s)
- Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jiayang Xu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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3
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Li J, Jin MK, Huang L, Liu ZF, Wang T, Chang RY, Op de Beeck M, Lambers H, Hui D, Xiao KQ, Chen QL, Sardans J, Peñuelas J, Yang XR, Zhu YG. Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland. ENVIRONMENT INTERNATIONAL 2024; 187:108688. [PMID: 38685158 DOI: 10.1016/j.envint.2024.108688] [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: 02/26/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.
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Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Lijie Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Zhan-Feng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tao Wang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Rui-Ying Chang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Michiel Op de Beeck
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia; Department of Plant Nutrition, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plan-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, TN, USA
| | - Ke-Qing Xiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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Zhao Z, Yang C, Gao B, Wu Y, Ao Y, Ma S, Jiménez N, Zheng L, Huang F, Tomberlin JK, Ren Z, Yu Z, Yu C, Zhang J, Cai M. Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115551. [PMID: 37832484 DOI: 10.1016/j.ecoenv.2023.115551] [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: 07/11/2023] [Revised: 09/20/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.
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Affiliation(s)
- Zhengzheng Zhao
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Chongrui Yang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Bingqi Gao
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Yushi Wu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Yue Ao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Shiteng Ma
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Núria Jiménez
- Department of Chemical Engineering, Vilanova i la Geltrú School of Engineering (EPSEVG), Universitat Politècnica de Catalunya·BarcelonaTech, Vilanova i la Geltrú 08800, Spain
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Feng Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | | | - Zhuqing Ren
- Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China; Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China.
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, PR China.
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5
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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6
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Wu J, Guo S, Li K, Li Z, Xu P, Jones DL, Wang J, Zou J. Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties. CHEMOSPHERE 2023; 336:139272. [PMID: 37343633 DOI: 10.1016/j.chemosphere.2023.139272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Guo
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejie Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pinshang Xu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, 6105, Australia
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
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Feng Y, Nuerla A, Tian M, Mamat A, Si A, Chang J, Abudureheman M, He C, Zhu J, Tong Z, Liu Z. Removal of chloramphenicol and resistance gene changes in electric-integrated vertical flow constructed wetlands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118143. [PMID: 37196621 DOI: 10.1016/j.jenvman.2023.118143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023]
Abstract
The performance of an electric-integrated vertical flow constructed wetland (E-VFCW) for chloramphenicol (CAP) removal, changes in microbial community structure, and the fate of antibiotic resistance genes (ARGs) were evaluated. CAP removal in the E-VFCW system was 92.73% ± 0.78% (planted) and 90.80% ± 0.61% (unplanted), both were higher than the control system which was 68.17% ± 1.27%. The contribution of anaerobic cathodic chambers in CAP removal was higher than the aerobic anodic chambers. Plant physiochemical indicators in the reactor revealed electrical stimulation increased oxidase activity. Electrical stimulation enhanced the enrichment of ARGs in the electrode layer of the E-VFCW system (except floR). Plant ARGs and intI1 levels were higher in the E-VFCW than in the control system, suggesting electrical stimulation induces plants to absorb ARGs, reducing ARGs in the wetland. The distribution of intI1 and sul1 genes in plants suggests that horizontal transfer may be the main mechanism dispersing ARGs in plants. High throughput sequencing analysis revealed electrical stimulation selectively enriched CAP degrading functional bacteria (Geobacter and Trichlorobacter). Quantitative correlation analysis between bacterial communities and ARGs confirmed the abundance of ARGs relates to the distribution of potential hosts and mobile genetic elements (intI1). E-VFCW is effective in treating antibiotic wastewater, however ARGs potentially accumulate.
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Affiliation(s)
- Yuran Feng
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Ailijiang Nuerla
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China.
| | - Menghan Tian
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Anwar Mamat
- School of Chemical Engineering and Technology, Xinjiang University, Urumqi, 830017, PR China
| | - Ang Si
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Jiali Chang
- Division of Environmental Engineering, School of Chemistry, Resources and Environment, Leshan Normal University, Sichuan, 614000, PR China
| | - Mukadasi Abudureheman
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Chaoyue He
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Jinjin Zhu
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Zhaohong Tong
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
| | - Zhaojiang Liu
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi, 830017, PR China; Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi, 830017, PR China
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8
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Fan X, Su J, Zhou S, An X, Li H. Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere. J Environ Sci (China) 2023; 127:508-518. [PMID: 36522081 DOI: 10.1016/j.jes.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 06/17/2023]
Abstract
The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.
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Affiliation(s)
- Xiaoting Fan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyidan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinli An
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Elyamine AM, Wang H, Oummu-Kulthum MAH, Raissa S, Nahdhoit AR, Meng S, Tao P, Hu Z. Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105920. [PMID: 36931048 DOI: 10.1016/j.marenvres.2023.105920] [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: 07/12/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r2 = 0.904), nitrogen (r2 = 0.72), phosphorus content (r2 = 0.62) and the water factor (r2 = 0.93). It was however highly and negatively correlated with the canopy cover (r2 = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China; Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Han Wang
- Huanhuai University, Zhumadian, 46000, China
| | | | - Sailine Raissa
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Ahamada Rachid Nahdhoit
- Institute of Graduate Studies, Fundamental and Industrial Microbiology, Istanbul University, 34134, Vezneciler Faith, Istanbul, Turkey
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China.
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10
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Li J, Daniell TJ, Jin MK, Chang RY, Wang T, Zhang J, Yang XR, Zhu YG. Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat. ENVIRONMENT INTERNATIONAL 2023; 174:107903. [PMID: 37058975 DOI: 10.1016/j.envint.2023.107903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The spread of antibiotic-resistance genes (ARGs) has posed a significant threat to human health over the past decades. Despite the fact that the phyllosphere represents a crucial pool of microorganisms, little is known about the profile and drivers of ARGs in less human interference natural habitats. In order to minimize the influence of environmental factors, here we collected leaf samples from the early-, middle- and late-successional stages across a primary vegetation successional sequence within 2 km, to investigate how the phyllosphere ARGs develop in natural habitats. Phyllosphere ARGs were determined using high-throughput quantitative PCR. Bacterial community and leaf nutrient content were also measured to assess their contribution to the phyllosphere ARGs. A total of 151 unique ARGs were identified, covering almost all recognized major antibiotic classes. We further found that there was some stochastic and a core set of the phyllosphere ARGs during the plant community succession process, due to the fluctuant phyllosphere habitat and specific selection effect of plant individuals. The ARG abundance significantly decreased due to the reduction of the phyllosphere bacterial diversity, community complexity, and leaf nutrient content during the plant community succession process. While the closer links between soil and fallen leaf resulted in a higher ARG abundance in leaf litter than in fresh leaf. In summary, our study reveals that the phyllosphere harbors a broad spectrum of ARGs in the natural environment. These phyllosphere ARGs are driven by various environmental factors, including the plant community composition, host leaf properties, and the phyllosphere microbiome.
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Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Rui-Ying Chang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Tao Wang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jing Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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11
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He Y, Yin X, Li F, Wu B, Zhu L, Ge D, Wang N, Chen A, Zhang L, Yan B, Huang H, Luo L, Wu G, Zhang J. Response characteristics of antibiotic resistance genes and bacterial communities during agricultural waste composting: Focusing on biogas residue combined with biochar amendments. BIORESOURCE TECHNOLOGY 2023; 372:128636. [PMID: 36657587 DOI: 10.1016/j.biortech.2023.128636] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
This research investigated biogas residue and biochar addition on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and changes in bacterial community during agricultural waste composting. Sequencing technique investigated bacterial community structure and ARGs, MGEs changes. Correlations among physicochemical factors, ARGs, MGEs, and bacterial community structure were determined using redundancy analysis. Results confirmed that biochar and biogas residue amendments effectively lowered the contents of ARGs and MGEs. The main ARGs detected was sul1. Proteobacteria and Firmicutes were the main host bacteria strongly associated with the dissemination of ARGs. The dynamic characteristics of the bacterial community were strongly correlated with pile temperature and pH (P < 0.05). Redundancy and network analysis revealed that nitrate, intI1, and Firmicutes mainly affected the in ARGs changes. Therefore, regulating these key variables would effectively suppress the ARGs spread and risk of compost use.
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Affiliation(s)
- Yuewei He
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Xiaowei Yin
- POWERCHINA Zhongnan Engineering Corporation Limited, Changsha 410014, Hunan, China
| | - Fanghong Li
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China; South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the PR China, Guangzhou 510655, China
| | - Bo Wu
- POWERCHINA Zhongnan Engineering Corporation Limited, Changsha 410014, Hunan, China
| | - Ling Zhu
- POWERCHINA Zhongnan Engineering Corporation Limited, Changsha 410014, Hunan, China
| | - Dabing Ge
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Nanyi Wang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Lihua Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Genyi Wu
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, Hunan, China; POWERCHINA Zhongnan Engineering Corporation Limited, Changsha 410014, Hunan, China; Yuelu Mountain Laboratory, Hunan Agricultural University Area, Changsha 410000, Hunan, China.
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12
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Wu RA, Feng J, Yue M, Liu D, Ding T. Overuse of food-grade disinfectants threatens a global spread of antimicrobial-resistant bacteria. Crit Rev Food Sci Nutr 2023; 64:6870-6879. [PMID: 36756870 DOI: 10.1080/10408398.2023.2176814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Food-grade disinfectants are extensively used for microbial decontamination of food processing equipment. In recent years, food-grade disinfectants have been increasingly used. However, the overuse of disinfectants causes another major issue, which is the emergence and spread of antimicrobial-resistant bacteria on a global scale. As the ongoing pandemic takes global attention, bacterial infections with antibiotic resistance are another ongoing pandemic that often goes unnoticed and will be the next real threat to humankind. Here, the effects of food-grade disinfectant overuse on the global emergence and spread of antimicrobial-resistant bacteria were reviewed. It was found that longtime exposure to the most common food-grade disinfectants promoted resistance to clinically important antibiotics in pathogenic bacteria, namely cross-resistance. Currently, the use of disinfectants is largely unregulated. The mechanisms of cross-resistance are regulated by intrinsic molecular mechanisms including efflux pumps, DNA repair system, modification of the molecular target, and metabolic adaptation. Cross-resistance can also be acquired by mobile genetic elements. Long-term exposure to disinfectants has an impact on the dissemination of antimicrobial resistance in soil, plants, animals, water, and human gut environments.
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Affiliation(s)
- Ricardo A Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Jinsong Feng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Min Yue
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Ningbo Research Institute, Zhejiang University, Ningbo, China
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13
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Yu Y, Zhang Q, Zhang Z, Zhou S, Jin M, Zhu D, Yang X, Qian H, Lu T. Plants select antibiotic resistome in rhizosphere in early stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159847. [PMID: 36461576 DOI: 10.1016/j.scitotenv.2022.159847] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Mingkang Jin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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14
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Sun Y, Li X, Ding C, Pan Q, Wang J. Host species and microplastics differentiate the crop root endophytic antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130091. [PMID: 36206714 DOI: 10.1016/j.jhazmat.2022.130091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/18/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The increasing One-Health concept calls for a more in-depth understanding of the dissemination of antibiotic resistance in plant microbiomes. While there is considerable published evidence that microplastics can promote the spread of antibiotic resistance genes (ARGs) in the environment, whether and how microplastics impact the plant endophytic resistome are largely unknown. Here we examined the ARGs along the soil-root continuum of maize and wheat under the pressure of microplastics. Amendment with heavy metals was also included as they can apply the selective pressure for ARG spread as well. The crop species and genotypes had significant effects on the root endophytic ARG abundance and diversity. The greatest ARG abundance was observed in the maize ZD958 endophytes (0.215 copies per 16S rRNA gene), followed by the maize XY335 (0.092 copies per 16S rRNA gene). For each crop genotype, amendment with microplastics and heavy metals significantly increased the ARG abundances and changed their profiles in root endophytes. The endophytic ARG variances were closely associated with the endophytic microbiome, the rhizosphere bacterial communities and resistome. Additionally, the level of endophytic ARGs was positively relevant to the abundance of mobile genetic elements (MGEs). These findings suggested that the root endophytic resistome was primarily affected by the crop species, and microplastics might show enhancement effects on the endophytic resistome via changing the root-associated microbiome and facilitating the MGE mediation. Overall, this study, for the first time, highlights the root endophytic ARG emergence and dissemination induced by microplastics.
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Affiliation(s)
- Yuanze Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinfei Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Changfeng Ding
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingchun Pan
- College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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15
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Zeng J, Li Y, Jin G, Su JQ, Yao H. Short-Term Benzalkonium Chloride (C 12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15054-15063. [PMID: 36069710 DOI: 10.1021/acs.est.2c04730] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C12) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg-1) and gradient concentrations of BC (0-100 mg kg-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.
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Affiliation(s)
- Jieyi Zeng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Guoping Jin
- Ningbo No. 9 Hospital, Ningbo 315020, People's Republic of China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, People's Republic of China
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16
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Sanz C, Casadoi M, Tadic Đ, Pastor-López EJ, Navarro-Martin L, Parera J, Tugues J, Ortiz CA, Bayona JM, Piña B. Impact of organic soil amendments in antibiotic levels, antibiotic resistance gene loads, and microbiome composition in corn fields and crops. ENVIRONMENTAL RESEARCH 2022; 214:113760. [PMID: 35753374 DOI: 10.1016/j.envres.2022.113760] [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: 02/25/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
The potential spreading of antibiotic resistance genes (ARG) into agricultural fields and crops represent a fundamental limitation on the use of organic fertilization in food production systems. We present here a study of the effect of spreading four types of organic soil amendments (raw pig slurry, liquid and solid fractions, and a digested derivative) on demonstrative plots in two consecutive productive cycles of corn harvest (Zea mays), using a mineral fertilizer as a control, following the application of organic amendments at 32-62 T per ha (150 kg total N/ha) and allowing 5-8 months between fertilization and harvest. A combination of qPCR and high-throughput 16S rDNA sequencing methods showed a small, but significant impact of the fertilizers in both ARG loads and microbiomes in soil samples, particularly after the second harvesting cycle. The slurry solid fraction showed the largest impact on both ARG loads and microbiome variation, whereas its digestion derivatives showed a much smaller impact. Soil samples with the highest ARG loads also presented increased levels of tetracyclines, indicating a potential dual hazard by ARG and antibiotic residues linked to some organic amendments. Unlike soils, no accumulation of ARG or antibiotics was observed in corn leaves (used as fodder) or grains, and no grain sample reached detection limits for neither parameter. These results support the use of organic soil amendments in corn crops, while proposing the reduction of the loads of ARGs and antibiotics from the fertilizers to greatly reduce their potential risk.
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Affiliation(s)
- Claudia Sanz
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | - Marta Casadoi
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | - Đorde Tadic
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | | | | | - Joan Parera
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | - Jordi Tugues
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | - Carlos A Ortiz
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | | | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain.
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17
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Zheng F, Zhou GW, Zhu D, Neilson R, Zhu YG, Chen B, Yang XR. Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14904-14912. [PMID: 35917301 DOI: 10.1021/acs.est.1c08733] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.
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Affiliation(s)
- Fei Zheng
- School of Life Sciences, Hebei University, Baoding 071002, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guo-Wei Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, United Kingdom
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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Wang F, Sun R, Hu H, Duan G, Meng L, Qiao M. The overlap of soil and vegetable microbes drives the transfer of antibiotic resistance genes from manure-amended soil to vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154463. [PMID: 35276164 DOI: 10.1016/j.scitotenv.2022.154463] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Livestock manure, as a major source of antibiotic resistance genes (ARGs), could further transfer ARGs from soil to vegetables when it's used as fertilizer in field and then pose threat to human health. Meanwhile, manure inputs and vegetable planting also affect soil bacterial communities, but these effects on the transmission of ARGs from soil to vegetable is still lacking. Here, lettuce and endive were cultivated in manure-amended soils using pot experiment. The distribution of bacterial community, ARGs and intI1 gene were studied in manure-amended soil and vegetable roots and leaves at harvest. High-throughput sequencing analysis demonstrated that planting vegetables exerted significant effect on soil bacterial communities, which partly explained the decrease of certain ARGs and the intI1 gene in planted soil than in control soil. ARGs in vegetable and soil were interconnected. The bacterial community compositions among root endophyte, leaf endophyte, and phyllosphere were varied by Hierarchical clustering analysis. Higher abundance of shared bacterial taxa was found between root endophytes and soil microbes, which could lead to a relative higher detection frequency of ARGs in root endophyte. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were dominant in the plant endophyte and phyllosphere microbes and had intensive correlations with ARGs. Taken together, our findings provided valuable insights into the role of bacterial community structure in the dissemination of ARGs from manure-amended soil to vegetables.
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Affiliation(s)
- Fenghua Wang
- Hebei Key Laboratory of Environmental Change and Ecological Construction, Hebei Experimental Teaching Demonstrating Center of Geographical Science, School of Geographical Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Liang Meng
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China; Shanghai Wetland Ecosystem National Observation and Research Station in the Eco-friendly Integration Demonstration Zone of the Yangtze River Delta, Shanghai 201722, China
| | - Min Qiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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19
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Yin Y, Zhu D, Yang G, Su J, Duan G. Diverse antibiotic resistance genes and potential pathogens inhabit in the phyllosphere of fresh vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152851. [PMID: 34990692 DOI: 10.1016/j.scitotenv.2021.152851] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Fresh vegetables are considered as a reservoir of pathogenic bacteria and antibiotic resistance genes (ARGs), which are the emerging environmental contaminants, posing increasing concerned risk to human health. However, the prevalence of pathogens in phyllosphere of fresh vegetables, as well as the association of ARGs with pathogenic bacteria, have not been well elaborated. In this study, we explored the structure of microbial communities and ARGs through high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing, and characterized the microorganisms resisting to antibiotics by pure culture. From phyllosphere of six different kinds of vegetables, 205 ARGs were detected and genes for multidrug resistance was the most abundant. The predominant potential pathogens were classified to Pseudomonas, Klebsiella, and Acinetobacter genera, which carried various ARGs such as multidrug and beta-lactam resistance genes presumedly. Among six kinds of vegetables, Lactuca sativa var. asparagina carried the highest abundance of potential pathogens and ARGs, while Allium sativum L harbored the lowest abundance of pathogens and ARGs. In addition, various culturable bacteria resisting to colistin or meropenem could be isolated from all vegetables, remarkably, all the isolates resistant to both antibiotics are potential pathogens. Our study highlighted the risks of pathogens and ARGs from raw vegetables to consumers, characterized their structure patterns among different vegetables, and analyzed the potential mechanisms regulating phyllosphere pathogens and resistome of fresh vegetables, which would be helpful for reducing the microbial risk from vegetable ingestion.
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Affiliation(s)
- Yue Yin
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Yang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jianqiang Su
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guilan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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21
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Deng B, Li W, Lu H, Zhu L. Film mulching reduces antibiotic resistance genes in the phyllosphere of lettuce. J Environ Sci (China) 2022; 112:121-128. [PMID: 34955195 DOI: 10.1016/j.jes.2021.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 06/14/2023]
Abstract
Phyllosphere is an important reservoir of antibiotic resistance genes (ARGs), but the transfer mechanism of ARGs from soil and air to phyllosphere remains unclear. This study demonstrated that soil-air-phyllosphere was the dominant ARG transfer pathway, and blocking it by film mulching can reduce typical phyllosphere ARGs in lettuce by 80.7% - 98.7% (89.5% on average). To further eliminate phyllosphere ARGs in lettuce grown with film mulching, the internal soil-endosphere-phyllosphere transfer pathway deserves more attention. We analyzed the ARG hosts and the resistome in lettuce rhizosphere and phyllosphere with film mulching via hybrid Illumina-Nanopore sequencing. Pseudomonas sp. 7SR1 was more abundant than other ARG hosts, accounting for 1.0% and 47.1% of the total bacteria in rhizosphere and phyllosphere, respectively. The species has flagella that can promote mobility and can excrete extracellular polymeric substances and/or surfactant-like microbial products, which benefits its colonization in the phyllosphere. Impeding the migration of Pseudomonas sp. 7SR1 via the soil-endosphere-phyllosphere pathway would be effective to further reduce ARGs in phyllosphere. Multidrug resistant genes were predominant in phyllosphere (40.3% of the total), and 87.6% of the phyllosphere ARGs were located on chromosomes, indicating relatively low horizontal gene transfer (HGT) potentials. This study provides insights into the transfer mechanism, hosts, and control strategies of phyllosphere ARGs in typical plants.
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Affiliation(s)
- Beiqi Deng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process andControl, Hangzhou, 310058, China
| | - Wen Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process andControl, Hangzhou, 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process andControl, Hangzhou, 310058, China.
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22
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Cui E, Cui B, Fan X, Li S, Gao F. Ryegrass (Lolium multiflorum L.) and Indian mustard (Brassica juncea L.) intercropping can improve the phytoremediation of antibiotics and antibiotic resistance genes but not heavy metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147093. [PMID: 33895506 DOI: 10.1016/j.scitotenv.2021.147093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/19/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Lolium multiflorum and Brassica juncea display phytoremediation potential for heavy metals and antibiotics pollution. However, there is limited understanding of their function in removing combined pollutants (heavy metals, antibiotics and antibiotic resistance genes (ARGs)) under different cropping patterns. Sole cropping had little effect on heavy metals, but reduced antibiotics by 2.46%-84.88% and increased ARGs by 15.96%-33.82%. Intercropping was more beneficial to soil remediation and plant accumulation of L. multiflorum, and further increased the remediation of antibiotics by 2.38%-54.40%. Members of phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) were mainly responsible for most antibiotics removal. Compared with sole cropping, intercropping reduced more ARGs abundance in rhizosphere soil for L. multiflorum (20.43%) and in bulk soil for B. juncea (23.22%). Mobile genetic elements (MGEs) played a significant role in the variation of ARGs. Further, sample type showed a higher indirect negative impact on ARGs by mainly affecting soil properties and bacterial community, and the co-occurrence between the bacterial community and ARGs in bulk soil was more complex than that in rhizosphere soil. Together these results suggest that phytoremediation of combined soil pollution was positive but limited, and intercropping resulted in enhanced removal efficiency when compared with sole cropping.
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Affiliation(s)
- Erping Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Bingjian Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Songjing Li
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Feng Gao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
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23
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Guo Y, Qiu T, Gao M, Sun Y, Cheng S, Gao H, Wang X. Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125595. [PMID: 34088171 DOI: 10.1016/j.jhazmat.2021.125595] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.
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Affiliation(s)
- Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanmei Sun
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, China
| | - Shoutao Cheng
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haoze Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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24
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Zhu D, Delgado-Baquerizo M, Su JQ, Ding J, Li H, Gillings MR, Penuelas J, Zhu YG. Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7445-7455. [PMID: 33977709 DOI: 10.1021/acs.est.1c00811] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Manuel Delgado-Baquerizo
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/Tulipán s/n, 28933 Móstoles, Spain
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Josep Penuelas
- CSIC, Global Ecology Unit, CREAF- CSIC-UAB, Bellaterra, Barcelona, Catalonia 08193, Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia 08193, Spain
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
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25
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Yan ZZ, Chen QL, Li CY, Thi Nguyen BA, Zhu YG, He JZ, Hu HW. Biotic and abiotic factors distinctly drive contrasting biogeographic patterns between phyllosphere and soil resistomes in natural ecosystems. ISME COMMUNICATIONS 2021; 1:13. [PMID: 36721011 PMCID: PMC9645249 DOI: 10.1038/s43705-021-00012-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 02/03/2023]
Abstract
The phyllosphere and soil are two of the most important reservoirs of antibiotic resistance genes (ARGs) in terrestrial ecosystems. However, comparative studies on the biogeographic patterns of ARGs in these two habitats are lacking. Based on the construction of ARG abundance atlas across a > 4,000 km transect in eastern and northern Australia, we found contrasting biogeographic patterns of the phyllosphere and soil resistomes, which showed their distinct responses to the biotic and abiotic stresses. The similarity of ARG compositions in soil, but not in the phyllosphere, exhibited significant distance-decay patterns. ARG abundance in the phyllosphere was mainly correlated with the compositions of co-occurring bacterial, fungal and protistan communities, indicating that biotic stresses were the main drivers shaping the phyllosphere resistome. Soil ARG abundance was mainly associated with abiotic factors including mean annual temperature and precipitation as well as soil total carbon and nitrogen. Our findings demonstrated the distinct roles of biotic and abiotic factors in shaping resistomes in different environmental habitats. These findings constitute a major advance in our understanding of the current environmental resistomes and contribute to better predictions of the evolution of environmental ARGs by highlighting the importance of habitat difference in shaping environmental resistomes.
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Affiliation(s)
- Zhen-Zhen Yan
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Qing-Lin Chen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Chao-Yu Li
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Bao-Anh Thi Nguyen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
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Pang Z, Chen J, Wang T, Gao C, Li Z, Guo L, Xu J, Cheng Y. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:621276. [PMID: 33737943 PMCID: PMC7961088 DOI: 10.3389/fpls.2021.621276] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 05/09/2023]
Abstract
Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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