151
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Tuo X, Gu J, Wang X, Sun Y, Duan M, Sun W, Yin Y, Guo A, Zhang L. Prevalence of quinolone resistance genes, copper resistance genes, and the bacterial communities in a soil-ryegrass system co-polluted with copper and ciprofloxacin. CHEMOSPHERE 2018; 197:643-650. [PMID: 29407828 DOI: 10.1016/j.chemosphere.2018.01.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
The presence of high concentrations of residual antibiotics and antibiotic resistance genes (ARGs) in soil may pose potential health and environmental risks. This study investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, copper resistance genes (CRGs), and the bacterial communities in a soil-ryegrass pot system co-polluted with copper and ciprofloxacin (CIP; 0, 20, or 80 mg kg-1 dry soil). Compared with the samples on day 0, the total relative abundances of the PMQR genes and mobile genetic elements (MGEs) were reduced significantly by 80-89% in the ryegrass and soil by the cutting stage (after 75 days). The abundances of PMQR genes and MGEs were reduced by 63-81% in soil treated with 20 mg kg-1 CIP compared with the other treatments, but the abundances of CRGs increased by 18-42%. The presence of 80 mg kg-1 CIP affected the microbial community structure in the soil by increasing the abundances of Acidobacteria and Thaumarchaeota, but decreasing those of Firmicutes. Redundancy analysis indicated that the pH and microbial composition were the main factors that affected the variations in PMQR genes, MGEs, and CRGs, where they could explain 42.2% and 33.3% of the variation, respectively. Furthermore, intI2 may play an important role in the transfer of ARGs. We found that 80 mg kg-1 CIP could increase the abundances of ARGs and CRGs in a soil-ryegrass pot system.
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Affiliation(s)
- Xiaxia Tuo
- 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; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - YiXin Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Manli Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanan Yin
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Aiyun Guo
- 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
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152
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Xiang Q, Chen QL, Zhu D, An XL, Yang XR, Su JQ, Qiao M, Zhu YG. Spatial and temporal distribution of antibiotic resistomes in a peri-urban area is associated significantly with anthropogenic activities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 235:525-533. [PMID: 29324382 DOI: 10.1016/j.envpol.2017.12.119] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 05/11/2023]
Abstract
With the rapid development of urbanization and industrialization, the peri-urban areas are often the sites for waste dumps, which may exacerbate the occurrence and spread of antibiotic resistance from waste to soil bacteria. However, the profiles of antibiotic resistomes and the associated factors influencing their dissemination in peri-urban areas have not been fully explored. Here, we characterized the antibiotic resistance genes (ARGs) in peri-urban arable and pristine soils in four seasons at the watershed scale, by using high-throughput qPCR. ARGs in peri-urban soils were diverse and abundant, with a total of 222 genes were detected in the peri-urban soil samples. The arable soil harbored more diverse ARGs compared to the pristine soils, and nearly all the ARGs detected in the pristine soils were also detected in the farmlands. A random forest prediction showed that the overall patterns of ARGs clustered closely with the landuse type. Mantel test and partial redundancy analysis indicated that bacterial community variation is a major contributor to antibiotic resistome alteration. Significant positive correlation was found between the abundance of ARGs and mobile genetic elements (MGEs), suggesting potential mobility of ARGs in peri-urban areas. Our results extend knowledge of the resistomes compositions in peri-urban areas, and suggest that anthropogenic activities driving its spatial and temporal distribution.
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Affiliation(s)
- Qian Xiang
- State Key Laboratory 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
| | - Qing-Lin Chen
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xin-Li An
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Min Qiao
- State Key Laboratory 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.
| | - 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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153
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Gou M, Hu HW, Zhang YJ, Wang JT, Hayden H, Tang YQ, He JZ. Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:1300-1310. [PMID: 28898936 DOI: 10.1016/j.scitotenv.2017.09.028] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/02/2017] [Accepted: 09/04/2017] [Indexed: 06/07/2023]
Abstract
Composting has been suggested as a potential strategy to eliminate antibiotic residues and pathogens in livestock manure before its application as an organic fertilizer in agro-ecosystems. However, the impacts of composting on antibiotic resistance genes (ARGs) in livestock manure and their temporal succession following the application of compost to land are not well understood. We examined how aerobic composting affected the resistome profiles of cattle manure, and by constructing laboratory microcosms we compared the effects of manure and compost application to agricultural soils on the temporal succession of a wide spectrum of ARGs. The high-throughput quantitative PCR array detected a total of 144 ARGs across all the soil, manure and compost samples, with Macrolide-Lincosamide-Streptogramin B, aminoglycoside, multidrug, tetracycline, and β-lactam resistance as the most dominant types. Composting significantly reduced the diversity and relative abundance of ARGs and mobile genetic elements (MGEs) in the cattle manure. In the 120-day microcosm incubation, the diversity and abundance of ARGs in manure-treated soils were significantly higher than those in compost-treated soils at the beginning of the experiment. The level of antibiotic resistance rapidly declined over time in all manure- and compost-treated soils, coupled with similar temporal patterns of manure- and compost-derived bacterial communities as revealed by SourceTracker analysis. The network analysis revealed more intensive interactions/associations among ARGs and MGEs in manure-treated soils than in compost-treated soils, suggesting that mobility potential of ARGs was lower in soils amended with compost. Our results provide evidence that aerobic composting of cattle manure may be an effective approach to mitigate the risk of antibiotic resistance propagation associated with land application of organic wastes.
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Affiliation(s)
- Min Gou
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia; College of Architecture and Environment, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Helen Hayden
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan 610065, China
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia; State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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154
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Wei Y, Zhao Y, Shi M, Cao Z, Lu Q, Yang T, Fan Y, Wei Z. Effect of organic acids production and bacterial community on the possible mechanism of phosphorus solubilization during composting with enriched phosphate-solubilizing bacteria inoculation. BIORESOURCE TECHNOLOGY 2018; 247:190-199. [PMID: 28950126 DOI: 10.1016/j.biortech.2017.09.092] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/12/2017] [Accepted: 09/15/2017] [Indexed: 05/22/2023]
Abstract
Enriched phosphate-solubilizing bacteria (PSB) agent were acquired by domesticated cultivation, and inoculated into kitchen waste composting in different stages. The effect of different treatments on organic acids production, tricalcium phosphate (TCP) solubilization and their relationship with bacterial community were investigated during composting. Our results pointed out that inoculation affected pH, total acidity and the production of oxalic, lactic, citric, succinic, acetic and formic acids. We also found a strong advantage in the solubilization of TCP and phosphorus (P) availability for PSB inoculation especially in the cooling stage. Redundancy analysis and structural equation models demonstrated inoculation by different methods changed the correlation of the bacterial community composition with P fractions as well as organic acids, and strengthened the cooperative function related to P transformation among species during composting. Finally, we proposed a possible mechanism of P solubilization with enriched PSB inoculation, which was induced by bacterial community and organic acids production.
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Affiliation(s)
- Yuquan Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingzi Shi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhenyu Cao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qian Lu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Tianxue Yang
- Laboratory of Water Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Yuying Fan
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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155
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Feng J, Li B, Jiang X, Yang Y, Wells GF, Zhang T, Li X. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. Environ Microbiol 2017; 20:355-368. [DOI: 10.1111/1462-2920.14009] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Jie Feng
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering; The University of Hong Kong; Hong Kong China
| | - Ying Yang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences; Sun Yat-sen University; Guangzhou China
| | - George F. Wells
- Department of Civil and Environmental Engineering; Northwestern University; Evanston IL USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering; The University of Hong Kong; Hong Kong China
| | - Xiaoyan Li
- Division of Energy & Environment, Graduate School at Shenzhen; Tsinghua University; China
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156
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Zhang J, Wang Z, Wang Y, Zhong H, Sui Q, Zhang C, Wei Y. Effects of graphene oxide on the performance, microbial community dynamics and antibiotic resistance genes reduction during anaerobic digestion of swine manure. BIORESOURCE TECHNOLOGY 2017; 245:850-859. [PMID: 28926918 DOI: 10.1016/j.biortech.2017.08.217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
The role of graphene oxide (GO) on anaerobic digestion (AD) of swine manure concerning the performance, microbial community and antibiotic resistance genes (ARGs) reduction was investigated. Results showed that methane production was reduced by 13.1%, 10.6%, 2.7% and 17.1% at GO concentration of 5mg/L, 50mg/L, 100mg/L and 500mg/L, respectively, but propionate degradation was enhanced along with GO addition. Both bacterial and archaeal community changed little after GO addition. AD could well reduce ARGs abundance, but it was deteriorated at the GO concentration of 50mg/L and 100mg/L and enhanced at 500mg/L, while no obvious changes at 5mg/L. Network and SEM analysis indicated that changes of each ARG was closely associated with variation of microbial community composition, environmental variables contributed most to the dynamics of ARGs indirectly, GO influenced the ARGs dynamics negatively and (heavy metal resistance genes (MRGs)) influenced the most directly.
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Affiliation(s)
- Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Ziyue Wang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yawei Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Hui Zhong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Qianwen Sui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Changping Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 100049 Beijing, China.
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157
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Zhang YJ, Hu HW, Gou M, Wang JT, Chen D, He JZ. Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1621-1632. [PMID: 28964602 DOI: 10.1016/j.envpol.2017.09.074] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 05/11/2023]
Abstract
Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days' incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs.
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Affiliation(s)
- Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Min Gou
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Deli Chen
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia; State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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158
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Han Y, Wang J, Zhao Z, Chen J, Lu H, Liu G. Fishmeal Application Induces Antibiotic Resistance Gene Propagation in Mariculture Sediment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10850-10860. [PMID: 28853291 DOI: 10.1021/acs.est.7b02875] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antibiotic resistance genes (ARGs) are globally prevalent in mariculture sediment, and their presence is an issue of concern in the context of antibiotic use. Although large amounts of fishmeal have been released into the sediment, the role of fishmeal in ARG dissemination remains unclear. In this study, high-throughput ARG profiles in representative fishmeal products and the impact of fishmeal on the sediment resistome were investigated. A total of 132 unique ARGs and 4 mobile genetic elements (MGEs) were detected in five fishmeal products. ARG abundance and diversity in the mariculture microcosm sediment were significantly increased by the addition of fishmeal, and trends in ARG patterns correlated with the resident bacterial community in sediment (P < 0.05). After DNase treatment of fishmeal removed 84.3% of total ARGs, the remaining nutrients in fishmeal increased the relative abundance but not the diversity of ARGs in microcosm sediment. Our study has revealed for the first time that fishmeal itself is a major reservoir for ARGs, and the shift in the bacterial community induced by the nutrients in fishmeal is the main driver shaping the resistome in mariculture microcosm sediment. Our findings caution against the previously unperceived risk of ARG propagation in fishmeal-receiving ecosystems.
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Affiliation(s)
- Ying Han
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
| | - Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology , Dalian 116024, Liaoning, P.R. China
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159
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Sun W, Xiao E, Xiao T, Krumins V, Wang Q, Häggblom M, Dong Y, Tang S, Hu M, Li B, Xia B, Liu W. Response of Soil Microbial Communities to Elevated Antimony and Arsenic Contamination Indicates the Relationship between the Innate Microbiota and Contaminant Fractions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9165-9175. [PMID: 28700218 DOI: 10.1021/acs.est.7b00294] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination. Comprehensive geochemical analyses and 16S rRNA gene amplicon sequencing demonstrated distinct soil taxonomic inventories depending on Sb and As contamination levels. Stochastic gradient boosting indicated that citric acid extractable Sb(V) and As(V) contributed 5% and 15%, respectively, to influencing the community diversity. Random forest predicted that low concentrations of Sb(V) and As(V) could enhance the community diversity but generally, the Sb and As contamination impairs microbial diversity. Co-occurrence network analysis indicated a strong correlation between the indigenous microbial communities and various Sb and As fractions. A number of taxa were identified as core genera due to their elevated abundances and positive correlation with contaminant fractions (total Sb and As concentrations, bioavailable Sb and As extractable fractions, and Sb and As redox species). Shotgun metagenomics indicated that Sb and As biogeochemical redox reactions may exist in contaminated soils. All these observations suggest the potential for bioremediation of Sb- and As-contaminated soils.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University , Guangzhou 510006, China
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences , Guiyang 550081, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University , Guangzhou 510006, China
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences , Guiyang 550081, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Qi Wang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650, China
| | - Max Häggblom
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Yiran Dong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Song Tang
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention , Beijing 100021, China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650, China
| | - Bingqing Xia
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650, China
| | - Wei Liu
- Water Resources Protection Bureau of Pearl River Water Resources Commission, Guangzhou 510611, China
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160
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Bai R, Wang JT, Deng Y, He JZ, Feng K, Zhang LM. Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers. Front Microbiol 2017; 8:945. [PMID: 28611747 PMCID: PMC5447084 DOI: 10.3389/fmicb.2017.00945] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.
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Affiliation(s)
- Ren Bai
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Ye Deng
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, MelbourneVIC, Australia
| | - Kai Feng
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of SciencesBeijing, China.,College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
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161
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Poole K. At the Nexus of Antibiotics and Metals: The Impact of Cu and Zn on Antibiotic Activity and Resistance. Trends Microbiol 2017; 25:820-832. [PMID: 28526548 DOI: 10.1016/j.tim.2017.04.010] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 12/14/2022]
Abstract
Environmental influences on antibiotic activity and resistance can wreak havoc with in vivo antibiotic efficacy and, ultimately, antimicrobial chemotherapy. In nature, bacteria encounter a variety of metal ions, particularly copper (Cu) and zinc (Zn), as contaminants in soil and water, as feed additives in agriculture, as clinically-used antimicrobials, and as components of human antibacterial responses. Importantly, there is a growing body of evidence for Cu/Zn driving antibiotic resistance development in metal-exposed bacteria, owing to metal selection of genetic elements harbouring both metal and antibiotic resistance genes, and metal recruitment of antibiotic resistance mechanisms. Many classes of antibiotics also form complexes with metal cations, including Cu and Zn, and this can hinder (or enhance) antibiotic activity. This review highlights the ways in which Cu/Zn influence antibiotic resistance development and antibiotic activity, and in so doing impact in vivo antibiotic efficacy.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada, K7L 3N6.
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162
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Wang S, Hou X, Su H. Exploration of the relationship between biogas production and microbial community under high salinity conditions. Sci Rep 2017; 7:1149. [PMID: 28442730 PMCID: PMC5430677 DOI: 10.1038/s41598-017-01298-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/24/2017] [Indexed: 11/25/2022] Open
Abstract
High salinity frequently causes inhibition and even failure in anaerobic digestion. To explore the impact of increasing NaCl concentrations on biogas production, and reveal the microbial community variations in response to high salinity stress, the Illumina high-throughput sequencing technology was employed. The results showed that a NaCl concentration of 20 g/L (H group) exhibited a similar level of VFAs and specific CO2 production rate with that in the blank group, thus indicating that the bacterial activity in acidogenesis might not be inhibited. However, the methanogenic activity in the H group was significantly affected compared with that in the blank group, causing a 42.2% decrease in CH4 production, a 37.12% reduction in the specific CH4 generation rate and a lower pH value. Illumina sequencing revealed that microbial communities between the blank and H groups were significantly different. Bacteroides, Clostridium and BA021 uncultured were the dominant species in the blank group while some halotolerant genera, such as Thermovirga, Soehngenia and Actinomyces, dominated and complemented the hydrolytic and acidogenetic abilities in the H group. Additionally, the most abundant archaeal species included Methanosaeta, Methanolinea, Methanospirillum and Methanoculleus in both groups, but hydrogenotrophic methanogens showed a lower resistance to high salinity than aceticlastic methanogens.
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Affiliation(s)
- Shaojie Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xiaocong Hou
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Haijia Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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163
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Abstract
Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.
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164
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Hu HW, Wang JT, Li J, Shi XZ, Ma YB, Chen D, He JZ. Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:790-800. [PMID: 27977160 DOI: 10.1021/acs.est.6b03383] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heavy metal contamination is assumed to be a selection pressure on antibiotic resistance, but to our knowledge, evidence of the heavy metal-induced changes of antibiotic resistance is lacking on a long-term basis. Using quantitative PCR array and Illumina sequencing, we investigated the changes of a wide spectrum of soil antibiotic resistance genes (ARGs) following 4-5 year nickel exposure (0-800 mg kg-1) in two long-term experimental sites. A total of 149 unique ARGs were detected, with multidrug and β-lactam resistance as the most prevailing ARG types. The frequencies and abundance of ARGs tended to increase along the gradient of increasing nickel concentrations, with the highest values recorded in the treatments amended with 400 mg nickel kg-1 soil. The abundance of mobile genetic elements (MGEs) was significantly associated with ARGs, suggesting that nickel exposure might enhance the potential for horizontal transfer of ARGs. Network analysis demonstrated significant associations between ARGs and MGEs, with the integrase intI1 gene having the most frequent interactions with other co-occurring ARGs. The changes of ARGs were mainly driven by nickel bioavailability and MGEs as revealed by structural equation models. Taken together, long-term nickel exposure significantly increased the diversity, abundance, and horizontal transfer potential of soil ARGs.
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Affiliation(s)
- Hang-Wei Hu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Jing Li
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Xiu-Zhen Shi
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Yi-Bing Ma
- National Soil Fertility and Fertilizer Effects Long-term Monitoring Network, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Deli Chen
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
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165
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Knapp CW, Callan AC, Aitken B, Shearn R, Koenders A, Hinwood A. Relationship between antibiotic resistance genes and metals in residential soil samples from Western Australia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:2484-2494. [PMID: 27822686 PMCID: PMC5340841 DOI: 10.1007/s11356-016-7997-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 10/25/2016] [Indexed: 05/19/2023]
Abstract
Increasing drug-resistant infections have drawn research interest towards examining environmental bacteria and the discovery that many factors, including elevated metal conditions, contribute to proliferation of antibiotic resistance (AR). This study examined 90 garden soils from Western Australia to evaluate predictions of antibiotic resistance genes from total metal conditions by comparing the concentrations of 12 metals and 13 genes related to tetracycline, beta-lactam and sulphonamide resistance. Relationships existed between metals and genes, but trends varied. All metals, except Se and Co, were related to at least one AR gene in terms of absolute gene numbers, but only Al, Mn and Pb were associated with a higher percentage of soil bacteria exhibiting resistance, which is a possible indicator of population selection. Correlations improved when multiple factors were considered simultaneously in a multiple linear regression model, suggesting the possibility of additive effects occurring. Soil-metal concentrations must be considered when determining risks of AR in the environment and the proliferation of resistance.
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Affiliation(s)
- Charles W Knapp
- Department of Civil & Environmental Engineering, University of Strathclyde, Glasgow, Scotland, G1 1XJ, UK.
| | - Anna C Callan
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Beatrice Aitken
- Department of Civil & Environmental Engineering, University of Strathclyde, Glasgow, Scotland, G1 1XJ, UK
| | - Rylan Shearn
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Annette Koenders
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Andrea Hinwood
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, WA, 6027, Australia
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166
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Su JQ, Cui L, Chen QL, An XL, Zhu YG. Application of genomic technologies to measure and monitor antibiotic resistance in animals. Ann N Y Acad Sci 2016; 1388:121-135. [DOI: 10.1111/nyas.13296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Xin-Li An
- 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
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