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Zeng Q, Wu X, Song M, Jiang L, Zeng Q, Qiu R, Luo C. Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19957-19965. [PMID: 39213533 DOI: 10.1021/acs.jafc.4c04258] [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: 09/04/2024]
Abstract
Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.
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Affiliation(s)
- Qing Zeng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xueqing Wu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Qiaoyun Zeng
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Rongliang Qiu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Zhang Z, Zhao L, Yang J, Pang J, Lambers H, He H. Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22663-22678. [PMID: 38409385 DOI: 10.1007/s11356-024-32578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.
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Affiliation(s)
- Zekun Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Le Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Hans Lambers
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Honghua He
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Institute of Soil and Water Conservation, Yangling, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, Shaanxi, China.
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Wang X, Zhang L, Gu J, Feng Y, He K, Jiang H. Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121950. [PMID: 37279818 DOI: 10.1016/j.envpol.2023.121950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3--N 14.7% and NH4+-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.
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Affiliation(s)
- Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yucheng Feng
- Department of C, rop, Soil & Environmental Sciences (formerly Agronomy and Soils), Auburn University, Auburn, AL36849, USA
| | - Kai He
- Tobacco Monopoly Bureau (Branch), Longhui, Shaoyang, Hunan, 422208, China
| | - Haihong Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Kang Y, Xu W, Zhang Y, Tang X, Bai Y, Hu J. Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13292-13304. [PMID: 34585344 DOI: 10.1007/s11356-021-16676-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.
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Affiliation(s)
- Yijun Kang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Wenjie Xu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Yang Zhang
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Xingyao Tang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, People's Republic of China
| | - Yanchao Bai
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jian Hu
- Environmental Science & Engineering, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China.
- Yancheng Teachers University, 2 South Hope Avenue, Yancheng, Jiangsu, People's Republic of China, 224007.
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Wen X, Xu J, Xiang G, Cao Z, Yan Q, Mi J, Ma B, Zou Y, Zhang N, Liao X, Wang Y, Wu Y. Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112815. [PMID: 34562788 DOI: 10.1016/j.ecoenv.2021.112815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/03/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guangfeng Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Cao
- WENS Foodstuff Group Co., Ltd., Yunfu, Xinxing 527400, China
| | - Qiufan Yan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Na Zhang
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; Guangdong Engineering Technology Research Center of Harmless Treatment and Resource Utilization of Livestock Waste, Yunfu, Xinxing 527400, China.
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Tang X, Shen M, Zhang Y, Zhu D, Wang H, Zhao Y, Kang Y. The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities. CHEMOSPHERE 2021; 266:128985. [PMID: 33228990 DOI: 10.1016/j.chemosphere.2020.128985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.
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Affiliation(s)
- Xingyao Tang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Min Shen
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yanzhou Zhang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Dewei Zhu
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Huanli Wang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China
| | - Yongqiang Zhao
- Yancheng National Nature Reserve for Rare Birds, Yancheng, Jiangsu, PR China
| | - Yijun Kang
- Yancheng Bioengineering Research Center for 'Binhai Bai-shou-wu', Yancheng Teachers University, Yancheng, Jiangsu, PR China.
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Miller DN, Jurgens ME, Durso LM, Schmidt AM. Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements. Front Microbiol 2020; 11:611912. [PMID: 33391241 PMCID: PMC7772212 DOI: 10.3389/fmicb.2020.611912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/25/2020] [Indexed: 11/29/2022] Open
Abstract
Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; tet(D), tet(G), and tet(L) were detected in background soil while swine manure contained tet(A), tet(B), tet(C), tet(G), tet(M), tet(O), tet(Q), and tet(X). By day 120, the manure-borne tet(M) and tet(O) were still detected while tet(C), tet(D), tet(L), and tet(X) genes were detected less frequently. Other tet resistance genes were detected rarely, if at all. The sum of unique tet resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique tet resistance genes. Four resistance elements, intI1, blactx–m–32, sul(I), erm(B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (−1.53 to −3.92 log abundance in manure; −4.02 to <−6.7 log abundance in soil). In the mixed manure/soil, relative abundance of the four resistance elements decreased (0.87 to 1.94 log abundance) during the incubation largely because 16S rRNA genes increased by 1.21 log abundance. Throughout the incubation, the abundance of intI1, blactx–m–32, sul(I), and erm(B) per gram in soil amended with HLAS-treated manure was lower than in soil amended with raw manure. Under low initial soil moisture conditions, HLAS treatment reduced the abundance of intI1 and resulted in loss of blactx–m–32, sul(I), and erm(B)] compared to other treatment-moisture combinations. Although one might expect antibiotic resistance to be relatively unchanged after simulated winter manure application to soil, a variety of changes in diversity and relative abundance can be expected.
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Affiliation(s)
- Daniel N Miller
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | | | - Lisa M Durso
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | - Amy M Schmidt
- Department of Biological Systems Engineering, University of Nebraska, Lincoln, NE, United States
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Song M, Peng K, Jiang L, Zhang D, Song D, Chen G, Xu H, Li Y, Luo C. Alleviated Antibiotic-Resistant Genes in the Rhizosphere of Agricultural Soils with Low Antibiotic Concentration. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2457-2466. [PMID: 31995379 DOI: 10.1021/acs.jafc.9b06634] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The influence of the rhizosphere on the abundance and diversity of antibiotic resistance genes (ARGs) has been recognized but there is a lack of consensus because of broad ranges of plant species and antibiotic concentrations across different habitats and the elusive underlying mechanisms. Here, we profiled antibiotic concentrations and resistomes in the rhizosphere and bulk soils by cultivating 10 types of crops in manure-amended agricultural soils. Rhizosphere effects altered the antibiotic resistome structure, significantly increased the absolute abundance of the antibiotic resistome, and decreased their relative abundance, contrasting previous studies. Such plantation-driven variation in ARGs resulted from the boost of bacterial lineages with negative relationships with ARGs and the constraint of the potential ARG-hosts in the rhizosphere of plants cultivated in soils with low antibiotic concentrations as the selective pressure. This mechanism is not reported previously and deepens our understanding about the rhizosphere effects on ARGs.
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Affiliation(s)
- Mengke Song
- The College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Ke Peng
- The College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , China
| | - Dandan Song
- The College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Guoen Chen
- The College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Huijuan Xu
- The College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Yongtao Li
- Joint Institute for Environmental Research and Education , South China Agricultural University , Guangzhou 510642 , China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry , Chinese Academy of Sciences , Guangzhou 510640 , China
- Joint Institute for Environmental Research and Education , South China Agricultural University , Guangzhou 510642 , China
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Blau K, Jacquiod S, Sørensen SJ, Su JQ, Zhu YG, Smalla K, Jechalke S. Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil. Front Microbiol 2019; 10:725. [PMID: 31057496 PMCID: PMC6477490 DOI: 10.3389/fmicb.2019.00725] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/22/2019] [Indexed: 12/23/2022] Open
Abstract
Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene tetA(P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene tetA(P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.
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Affiliation(s)
- Khald Blau
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sven Jechalke
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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