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Zhang H, Ouyang W, Lin C, Wang L, Guo Z, Pei J, Zhang S, He M, Liu X. Anthropogenic activities drive the distribution and ecological risk of antibiotics in a highly urbanized river basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173596. [PMID: 38810736 DOI: 10.1016/j.scitotenv.2024.173596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Although antibiotics are widely detected in river water, their quantitative relationships with influencing factors in rivers remain largely unexplored. Here, 15 widely used antibiotics were comprehensively analyzed in the Dongjiang River of the Pearl River system. The total antibiotic concentration in river water ranged from 13.84 to 475.04 ng/L, with fluoroquinolones increasing from 11 % in the upstream to 38 % in the downstream. The total antibiotic concentration was high downstream and significantly correlated with the spatial distribution of population density, animal production, and land-use type. The total risk quotient of antibiotics for algae was higher than that for crustaceans and fish. Based on the optimized risk quotient method, amoxicillin, ofloxacin, and norfloxacin were identified as priority antibiotics. The key predictors of antibiotic levels were screened through Mantel test, correlation analysis, and multiple regression models. Water physicochemical parameters significantly impacted antibiotics and could be used as easy-to-measure surrogates associated with elevated antibiotics. Cropland negatively affected fluoroquinolones and sulfonamides, whereas urban land exerted positive impacts on fluoroquinolones, β-lactam, and sulfonamides. In the main stream, population, animal production, urbanization status, and economic development had key effects on the distribution of florfenicol, norfloxacin, ofloxacin, and sulfadiazine.
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Affiliation(s)
- He Zhang
- Advanced Interdisciplinary Institute of Environment and Ecology, Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning, Beijing Normal University, Zhuhai 519087, China; State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- Advanced Interdisciplinary Institute of Environment and Ecology, Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning, Beijing Normal University, Zhuhai 519087, China; State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Lei Wang
- Advanced Interdisciplinary Institute of Environment and Ecology, Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning, Beijing Normal University, Zhuhai 519087, China; State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Zewei Guo
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jietong Pei
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Shangwei Zhang
- Advanced Interdisciplinary Institute of Environment and Ecology, Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning, Beijing Normal University, Zhuhai 519087, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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2
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Wang S, Nie W, Gu Q, Wang X, Yang D, Li H, Wang P, Liao W, Huang J, Yuan Q, Zhou S, Ahmad I, Kotaro K, Chen G, Zhu B. Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database. WATER RESEARCH 2024; 256:121572. [PMID: 38621316 DOI: 10.1016/j.watres.2024.121572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.
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Affiliation(s)
- Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Qing Gu
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Xie Wang
- Southwest China Mountain Agricultural Environment Key Laboratory, Ministry of Agriculture and Rural Areas, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Shizishan Rd, Chengdu, 610066, China
| | - Danping Yang
- Observation and Research Station of Ecological Restoration for Chongqing Typical Mining Areas, Ministry of Natural Resources (Chongqing Institute of Geology and Mineral Resources), Chongqing, 401120. China
| | - Hongyu Li
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Huang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Quan Yuan
- School of Energy and Power Engineering, Xihua University, Chengdu, 610039, China
| | - Shengli Zhou
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Kiga Kotaro
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Lei L, Chen N, Chen Z, Zhao Y, Lin H, Li X, Hu W, Zhang H, Shi J, Luo Y. Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms. WATER RESEARCH 2024; 256:121584. [PMID: 38598950 DOI: 10.1016/j.watres.2024.121584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.
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Affiliation(s)
- Liusheng Lei
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Nan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Zeyou Chen
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Yirong Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Huai Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Xi Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Wenjin Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hanhui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Jingliang Shi
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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Wang C, Mao Y, Zhang L, Wei H, Wang Z. Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics. WATER RESEARCH 2024; 256:121583. [PMID: 38614031 DOI: 10.1016/j.watres.2024.121583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/06/2024] [Indexed: 04/15/2024]
Abstract
The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.
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Affiliation(s)
- Cong Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Mao
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Wei
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China.
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Makowska-Zawierucha N, Trzebny A, Zawierucha K, Manthapuri V, Bradley JA, Pruden A. Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients. GLOBAL CHANGE BIOLOGY 2024; 30:e17293. [PMID: 38687495 DOI: 10.1111/gcb.17293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress-response genes that might be co/cross-selected or co-transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run-off from glaciers could contribute to the release and spread of plasmid-related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean.
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Affiliation(s)
- Nicoletta Makowska-Zawierucha
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Vineeth Manthapuri
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - James A Bradley
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
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6
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Shuai X, Zhou Z, Zhu L, Achi C, Lin Z, Liu Z, Yu X, Zhou J, Lin Y, Chen H. Ranking the risk of antibiotic resistance genes by metagenomic and multifactorial analysis in hospital wastewater systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133790. [PMID: 38368689 DOI: 10.1016/j.jhazmat.2024.133790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Antimicrobial resistance poses a serious threat to human health. Hospital wastewater system (HWS) is an important source of antibiotic resistance genes (ARGs). The risk of ARGs in HWS is still an under-researched area. In this study, we collected publicly metagenomic datasets of 71 hospital wastewater samples from 18 hospitals in 13 cities. A total of 9838 contigs were identified to carry 383 unique ARGs across all samples, of which 2946 contigs were plasmid-like sequences. Concurrently, the primary hosts of ARGs within HWS were found to be Escherichia coli and Klebsiella pneumoniae. To further evaluate the risk of each ARG subtype, we proposed a risk assessment framework based on the importance of corresponding antibiotics as defined by the WHO and three other indicators - ARG abundance (A), mobility (M), and host pathogenicity (P). Ninety ARGs were identified as R1 ARGs having high-risk scores, which meant having a high abundance, high mobility, and carried by pathogens in HWS. Furthermore, 25% to 49% of genomes from critically important pathogens accessed from NCBI carried R1 ARGs. A significantly higher number of R1 ARGs was carried by pathogens in the effluents of municipal wastewater treatment plants from NCBI, highlighting the role of R1 ARGS in accelerating health and environmental risks.
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Affiliation(s)
- Xinyi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenchao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Chioma Achi
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, United Kingdom
| | - Zejun Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xi Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinyu Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanhan Lin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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7
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Yan D, Han Y, Zhong M, Wen H, An Z, Capo E. Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake. ENVIRONMENT INTERNATIONAL 2024; 186:108654. [PMID: 38621322 DOI: 10.1016/j.envint.2024.108654] [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: 01/22/2024] [Revised: 03/13/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.
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Affiliation(s)
- Dongna Yan
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710061, China
| | - Yongming Han
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710061, China; National Observation and Research Station of Regional Ecological Environment Change and Comprehensive Management in the Guanzhong Plain, Xi'an, Shaanxi 710061, China.
| | - Meifang Zhong
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, 907 36 Umeå, Sweden
| | - Hanfeng Wen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710061, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhisheng An
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710061, China
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, 907 36 Umeå, Sweden.
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Xie J, Chen C, Luo M, Peng X, Lin T, Chen D. Hidden dangers: High levels of organic pollutants in hadal trenches. WATER RESEARCH 2024; 251:121126. [PMID: 38237461 DOI: 10.1016/j.watres.2024.121126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
The "V"-shaped structure of hadal trenches acts as a natural collector of organic pollutants, drawing attention to the need for extensive research in these areas. Our review identifies significant concentrations of organic pollutants, including persistent organic pollutants, black carbon, antibiotic-resistant genes, and plastics, which often match those in industrialized regions. They may trace back to both human activities and natural sources, underscoring the trenches' critical role in ocean biogeochemical cycles. We highlight the complex lateral and vertical transport mechanisms within these zones. Advanced methodologies, including stable isotope analysis, biomarker identification, and chiral analysis within isotope-based mixing models, are crucial for discerning the origins and pathways of these pollutants. In forthcoming studies, we aim to explore advanced methods for precise pollutant tracing, develop predictive models to forecast the future distribution and impacts of pollutants in hadal zones and on the Earth's larger ecological systems.
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Affiliation(s)
- Jingqian Xie
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China.
| | - Chuchu Chen
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Min Luo
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaotong Peng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Tian Lin
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Duofu Chen
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
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9
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Yan J, Guo X, He M, Niu Z, Xu M, Peng B, Yang Y, Jin Z. Metals and microorganisms in a Maar lake sediment core indicating the anthropogenic impact over last 800 years. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168392. [PMID: 37956839 DOI: 10.1016/j.scitotenv.2023.168392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/31/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023]
Abstract
A closed Maar lake, receiving mostly atmospheric deposition, offers a unique setting for investigating the impact of human activities on the environment. In this study, we aimed to investigate the historical record of metals in core sediments of Maar Lake in Huguangyan (HGY), Southeast China, and elucidate the possible microbial responses to anthropogenic metal stress. Five stages were divided according to the historical record of metals and corresponding distribution of microbial community, among which Pb and Sn showed a peak value around 1760 CE, indicating the ancient mining and smelting activities. Since the 1980s, a substantial enrichment of metals such as Zn, As, Mo, Cd, Sn, Sb, and Pb was observed, due to the rapid industrial growth in China. In terms of microorganisms, Chloroflexi phylum, particularly dominated by Anaerolineales, showed significant correlations with Pb and Sn, and could potentially serve as indicator species for mining and smelting-related contamination. Desulfarculales and Desulfobacterales were found to be more prevalent in recent period and exhibited positive correlations with anthropogenic metals. Moreover, according to the multivariate regression modeling and variance decomposition analysis, Pb and Sn could regulate Anaerolineales and further pose impact on the carbon cycle; while sulfate-reducing bacteria (SRB) could response to anthropogenic metals and influence sulfur cycle. These findings provide new insights into the interaction between metals and microbial communities over human history.
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Affiliation(s)
- Jia Yan
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xingpan Guo
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Maoyong He
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
| | - Zuoshun Niu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Miao Xu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Bo Peng
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.
| | - Zhangdong Jin
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
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10
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Liu L, Yao Q, Jiang F, Cai Z, Meng M, Sun H, Zhang L, Gong J. Ultrasensitive Dual-Mode Visual/Photoelectrochemical Bioassay for Antibiotic Resistance Genes through Incorporating Rolling Circle Amplicons into a Tailored Nanoassembly. Anal Chem 2024. [PMID: 38329298 DOI: 10.1021/acs.analchem.3c04539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
As emerging contaminants in the environment, antibiotic resistance genes (ARGs) have aroused a global health crisis and posed a serious threat to ecological safety and human health. Thus, efficient and accurate onsite detection of ARGs is crucial for environmental surveillance. Here, we presented a colorimetric-photoelectrochemical (PEC) dual-mode bioassay for simultaneous detection of multiple ARGs by smartly incorporating rolling circle amplification (RCA) into a stimuli-responsive DNA nanoassembly, using the tetracycline resistance genes tetA and tetC as models. The tailored DNA nanoassembly containing RCA amplicons hybridized with specific signal probes: CuO nanoflowers-anchored signal DNA1 and HgO nanoparticles-anchored signal DNA2, respectively. Upon exposure to an acidic stimulus, numerous Cu2+ and Hg2+ were released, serving as the reporting agent of colorimetric/PEC dual-mode assay. The released Cu2+ and Hg2+ induced localized surface plasmon resonance shifts in Au nanorods and triangular Ag nanoplates through an etching process, respectively, enabling visual analysis of ARGs with distinguishing color changes. Meanwhile, numerous Cu2+ and Hg2+ triggered the amplified PEC variations via reacting with the photoactive layers of CuS/CdS and ZnS, respectively. Thus, a rapid and ultrasensitive colorimetric/PEC dual-mode detection of multiple ARGs was achieved with the detection limit down to 17.2 aM. Furthermore, such dual-mode bioassay could discriminate single-base mismatch and successfully determine ARGs in E. coli plasmids and sludge samples, holding great promise for point-of-care genetic diagnostics.
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Affiliation(s)
- Lijuan Liu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Qingfeng Yao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Fang Jiang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Zheng Cai
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Mingxia Meng
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hongwei Sun
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Lizhi Zhang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jingming Gong
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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11
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Han Z, Luan X, Feng H, Deng Y, Yang M, Zhang Y. Metagenomic insights into microorganisms and antibiotic resistance genes of waste antibiotic fermentation residues along production, storage and treatment processes. J Environ Sci (China) 2024; 136:45-55. [PMID: 37923454 DOI: 10.1016/j.jes.2022.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
Antibiotic fermentation residue (AFR) is nutrient-rich solid waste generated from fermentative antibiotic production process. It is demonstrated that AFR contains high-concentration of remaining antibiotics, and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals. However, the dominate microorganisms and antibiotic resistance genes (ARGs) in AFRs have not been adequately explored, hampering understanding on the potential antibiotic resistance risk development caused by AFRs. Herein, seven kinds of representative AFRs along their production, storage, and treatment processes were collected, and multiple methods including amplicon sequencing, metagenomic sequencing, and bioinformatic approaches were adopted to explore the biological characteristics of AFRs. As expected, antibiotic fermentation producer was found as the predominant species in raw AFRs, which were collected at the outlet of fermentation tanks. However, except for producer species, more environment-derived species persisted in stored AFRs, which were temporarily stored at a semi-open space. Lactobacillus genus, classified as Firmicutes phylum and Bacilli class, became predominant bacterial taxa in stored AFRs, which might attribute to its tolerance to high concentration of antibiotics. Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species (e.g., Lactobacillus genus) tended to carry ARGs conferring resistance to the remaining antibiotic. However, after thermal treatment, remaining antibiotic could be efficiently removed from AFRs, and microorganisms together with DNA could be strongly destroyed. In sum, the main risk from the AFRs was the remaining antibiotic, while environment-derived bacteria which tolerate extreme environment, survived in ARFs with high content antibiotics, and may carry ARGs. Thus, hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.
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Affiliation(s)
- Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haodi Feng
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanqin Deng
- Wuhan Agricultural Inspection Center, Wuhan 430016, China
| | - Min Yang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Li Y, Kan J, Liu F, Lian K, Liang Y, Shao H, McMinn A, Wang H, Wang M. Depth shapes microbiome assembly and network stability in the Mariana Trench. Microbiol Spectr 2024; 12:e0211023. [PMID: 38084983 PMCID: PMC10783068 DOI: 10.1128/spectrum.02110-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/08/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.
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Affiliation(s)
- Yi Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Pennsylvania, USA
| | - Feilong Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Kaiyue Lian
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
- UMT-OUC Joint Center for Marine Studies, Qingdao, China
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13
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Teixeira AM, Vaz-Moreira I, Calderón-Franco D, Weissbrodt D, Purkrtova S, Gajdos S, Dottorini G, Nielsen PH, Khalifa L, Cytryn E, Bartacek J, Manaia CM. Candidate biomarkers of antibiotic resistance for the monitoring of wastewater and the downstream environment. WATER RESEARCH 2023; 247:120761. [PMID: 37918195 DOI: 10.1016/j.watres.2023.120761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Urban wastewater treatment plants (UWTPs) are essential for reducing the pollutants load and protecting water bodies. However, wastewater catchment areas and UWTPs emit continuously antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with recognized impacts on the downstream environments. Recently, the European Commission recommended to monitor antibiotic resistance in UWTPs serving more than 100 000 population equivalents. Antibiotic resistance monitoring in environmental samples can be challenging. The expected complexity of these systems can jeopardize the interpretation capacity regarding, for instance, wastewater treatment efficiency, impacts of environmental contamination, or risks due to human exposure. Simplified monitoring frameworks will be essential for the successful implementation of analytical procedures, data analysis, and data sharing. This study aimed to test a set of biomarkers representative of ARG contamination, selected based on their frequent human association and, simultaneously, rare presence in pristine environments. In addition to the 16S rRNA gene, ten potential biomarkers (intI1, sul1, ermB, ermF, aph(3'')-Ib, qacEΔ1, uidA, mefC, tetX, and crAssphage) were monitored in DNA extracts (n = 116) from raw wastewater, activated sludge, treated wastewater, and surface water (upstream and downstream of UWTPs) samples collected in the Czech Republic, Denmark, Israel, the Netherlands, and Portugal. Each biomarker was sensitive enough to measure decreases (on average by up to 2.5 log-units gene copy/mL) from raw wastewater to surface water, with variations in the same order of magnitude as for the 16S rRNA gene. The use of the 10 biomarkers allowed the typing of water samples whose origin or quality could be predicted in a blind test. The results show that, based on appropriate biomarkers, qPCR can be used for a cost-effective and technically accessible approach to monitoring wastewater and the downstream environment.
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Affiliation(s)
- A Margarida Teixeira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - David Calderón-Franco
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands
| | - David Weissbrodt
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands; Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7034, Norway
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Stanislav Gajdos
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Giulia Dottorini
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Leron Khalifa
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal.
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14
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Li X, Xie J, Ding C, Du H, Gao S, Ma W, Liang F, Zhang H, Wang A. Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166055. [PMID: 37543322 DOI: 10.1016/j.scitotenv.2023.166055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/16/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.
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Affiliation(s)
- Xuan Li
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Jiahao Xie
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Cheng Ding
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China.
| | - Hongqiu Du
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Shuhong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
| | - Weixing Ma
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Feng Liang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; Center for Water and Environmental Technology, YCEST, Yancheng 224051, PR China
| | - Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, PR China
| | - Aijie Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, PR China
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15
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Wang C, Yang H, Liu H, Zhang XX, Ma L. Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking. WATER RESEARCH 2023; 246:120682. [PMID: 37832249 DOI: 10.1016/j.watres.2023.120682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10-4 to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.
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Affiliation(s)
- Chen Wang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Huiying Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Huafeng Liu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
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16
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Xu N, Qiu D, Zhang Z, Wang Y, Chen B, Zhang Q, Wang T, Hong W, Zhou NY, Penuelas J, Gillings M, Zhu YG, Qian H. A global atlas of marine antibiotic resistance genes and their expression. WATER RESEARCH 2023; 244:120488. [PMID: 37604017 DOI: 10.1016/j.watres.2023.120488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023]
Abstract
Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia 08193, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Catalonia 08193, Spain
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Yong-Guan Zhu
- Key Laboratory 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
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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17
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Akter S, Rahman MS, Ali H, Minch B, Mehzabin K, Siddique MM, Galib SM, Yesmin F, Azmuda N, Adnan N, Hasan NA, Rahman SR, Moniruzzaman M, Ahmed MF. Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast. Sci Rep 2023; 13:15976. [PMID: 37749192 PMCID: PMC10520010 DOI: 10.1038/s41598-023-43306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023] Open
Abstract
The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.
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Affiliation(s)
- Salma Akter
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hazrat Ali
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA
| | - Kaniz Mehzabin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Moradul Siddique
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Syed Md Galib
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farida Yesmin
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Nur A Hasan
- University of Maryland, College Park, MD, USA
| | | | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, USA.
| | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh.
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18
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Al-Sarawi HA, Habibi N, Uddin S, Jha AN, Al-Sarawi MA, Lyons BP. Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis. Antibiotics (Basel) 2023; 12:1366. [PMID: 37760663 PMCID: PMC10525739 DOI: 10.3390/antibiotics12091366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.
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Affiliation(s)
- Hanan A. Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait;
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait;
| | - Awadhesh N. Jha
- School of Biological Sciences, Plymouth University, Drake Circus, Plymouth PL4 8AA, UK;
| | - Mohammed A. Al-Sarawi
- Department of Earth & Environmental Sciences, Kuwait University, Faculty of Science, P.O. Box 5969, Safat 13060, Kuwait;
| | - Brett P. Lyons
- Research & Monitoring Coordination Nature Conservation Department, Neom 49625, Saudi Arabia;
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Yuan Q, Wang X, Fang H, Cheng Y, Sun R, Luo Y. Coastal mudflats as reservoirs of extracellular antibiotic resistance genes: Studies in Eastern China. J Environ Sci (China) 2023; 129:58-68. [PMID: 36804242 DOI: 10.1016/j.jes.2022.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/18/2023]
Abstract
Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems, little is known about the profiles of antibiotic resistance genes (ARGs) in this area. In this study, characteristics of typical ARGs, involving both intracellular (iARGs) and extracellular ARGs (eARGs) at different physical states, were explored in over 1000 km of coastal mudflats in Eastern China. Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles. The abundance of eARGs was significantly higher than that of iARGs (87.3% vs 12.7%), and their dominance was more significant than those in other habitats (52.7%-76.3%). ARG abundance, especially for eARGs, showed an increasing trend (p < 0.05) from southern (Nantong) to northern (Lianyungang) coastal mudflats. Higher salinity facilitated the transformation from iARGs to eARGs, and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats. This study addresses the neglected function of coastal mudflats as eARGs reservoirs.
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Affiliation(s)
- Qingbin Yuan
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xiaolin Wang
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Hui Fang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yuan Cheng
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ruonan Sun
- Department of Civil and Environmental Engineering, Rice University, Houston 77005, USA
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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20
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Zeng J, Pan Y, Hu R, Liu F, Gu H, Ding J, Liu S, Liu S, Yang X, Peng Y, Tian Y, He Q, Wu Y, Yan Q, Shu L, He Z, Wang C. The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131974. [PMID: 37406521 DOI: 10.1016/j.jhazmat.2023.131974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.
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Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Jijuan Ding
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN, USA
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510530, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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21
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Wu C, Zhang G, Zhang K, Sun J, Cui Z, Guo Y, Liu H, Xu W. Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118132. [PMID: 37263036 DOI: 10.1016/j.jenvman.2023.118132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/03/2023]
Abstract
Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.
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Affiliation(s)
- Chao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Guicheng Zhang
- Research Centre for Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Kai Zhang
- National Observation and Research Station of Coastal Ecological Environments in Macao, Macao Environmental Research Institute, Macau University of Science and Technology, Macao, 999078, China
| | - Jun Sun
- Research Centre for Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 510635, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China.
| | - Zhengguo Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
| | - Yiyan Guo
- Research Centre for Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Haijiao Liu
- Research Centre for Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenzhe Xu
- Research Centre for Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China
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22
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Li Y, Kong F, Li S, Wang J, Hu J, Chen S, Chen Q, Li Y, Ha X, Sun W. Insights into the driving factors of vertical distribution of antibiotic resistance genes in long-term fertilized soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131706. [PMID: 37247491 DOI: 10.1016/j.jhazmat.2023.131706] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in soils has aroused wide attention. However, the influence of long-term fertilization on the distribution of ARGs in different soil layers and its dominant drivers remain largely unknown. In this study, a total of 203 ARGs were analyzed in greenhouse vegetable soils (0-100 cm from a 13-year field experiment applied with different fertilizers (control, chemical fertilizer, organic manure, and mixed fertilizer). Compared with unfertilized and chemically fertilized soils, manure application significantly increased the abundance and alpha diversity of soil ARGs, where the assembly of ARG communities was strongly driven by stochastic processes. The distribution of ARGs was significantly driven by manure application within 60 cm, while it was insignificantly changed in soil below 60 cm under different fertilization regimes. The inter-correlations of ARGs with mobile genetic elements (MGEs) and microbiota were strengthened in manured soil, indicating manure application posed a higher risk for ARGs diffusion in subsurface soil. Bacteria abundance and MGEs directly influenced ARG abundance and composition, whereas soil depth and manure application indirectly influenced ARG abundance and composition by affecting antibiotics. These results strengthen our understanding of the long-term anthropogenic influence on the vertical distribution of soil ARGs and highlight the ecological risk of ARGs in subsurface soil induced by long-term manure application.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Fanguang Kong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Yantai Institute of China Agricultural University, Yantai 264670, 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
| | - Jingrun Hu
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shuo Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Chen
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanming Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xuejiao Ha
- Planting Technology Promotion Station of Daxing District, Beijing 102600, China
| | - Weiling Sun
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
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23
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Hu Z, Yang L, Liu Z, Han J, Zhao Y, Jin Y, Sheng Y, Zhu L, Hu B. Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163598. [PMID: 37094669 PMCID: PMC10122561 DOI: 10.1016/j.scitotenv.2023.163598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/01/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
During COVID-19 pandemic, chemicals from excessive consumption of pharmaceuticals and disinfectants i.e., antibiotics, quaternary ammonium compounds (QACs), and trihalomethanes (THMs), flowed into the urban environment, imposing unprecedented selective pressure to antimicrobial resistance (AMR). To decipher the obscure character pandemic-related chemicals portrayed in altering environmental AMR, 40 environmental samples covering water and soil matrix from surroundings of Wuhan designated hospitals were collected on March 2020 and June 2020. Chemical concentrations and antibiotic resistance gene (ARG) profiles were revealed by ultra-high-performance liquid chromatography-tandem mass spectrometry and metagenomics. Selective pressure from pandemic-related chemicals ascended by 1.4-5.8 times in March 2020 and then declined to normal level of pre-pandemic period in June 2020. Correspondingly, the relative abundance of ARGs under increasing selective pressure was 20.1 times that under normal selective pressure. Moreover, effect from QACs and THMs in aggravating the prevalence of AMR was elaborated by null model, variation partition and co-occurrence network analyses. Pandemic-related chemicals, of which QACs and THMs respectively displayed close interaction with efflux pump genes and mobile genetic elements, contributed >50 % in shaping ARG profile. QACs bolstered the cross resistance effectuated by qacEΔ1 and cmeB to 3.0 times higher while THMs boosted horizon ARG transfer by 7.9 times for initiating microbial response to oxidative stress. Under ascending selective pressure, qepA encoding quinolone efflux pump and oxa-20 encoding β-lactamases were identified as priority ARGs with potential human health risk. Collectively, this research validated the synergistic effect of QACs and THMs in exacerbating environmental AMR, appealing for the rational usage of disinfectants and the attention for environmental microbes in one-health perspective.
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Affiliation(s)
- Zhichao Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jian Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yihao Jin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaqi Sheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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Xie J, Zhang G, Wu Q, Luo M, Chen D, Zhang Y, He L, Li Y, Zhang Q, Lin T, Jiang G. First evidence and potential sources of novel brominated flame retardants and BDE 209 in the deepest ocean. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130974. [PMID: 36860051 DOI: 10.1016/j.jhazmat.2023.130974] [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: 10/21/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Organic anthropogenic pollutants reach even the deepest parts of the oceans, i.e., the hadal trenches. We here presented the concentrations, influencing factors, and potential sources of polybrominated diphenyl ethers (PBDEs) and novel brominated flame retardants (NBFRs) in hadal sediments and amphipods from the Mariana, Mussau and New Britain trenches. Results showed that BDE 209 was the dominant PBDEs congener and DBDPE was the dominant NBFRs. No significant correlation was found between TOC contents and PBDEs or NBFRs levels in sediment. Lipid content and body length were the potential important factors affecting variation in pollutant concentrations in the carapace & muscle of amphipods, while the pollution levels of viscera were mainly affected by the sex and lipid content. PBDEs and NBFRs might reach trench surface seawater through long-range atmospheric transport and oceans currents but with little contribution from the Great Pacific Garbage Patch. Determination of carbon and nitrogen isotopes indicated that the pollutants were transported and accumulated in amphipods and sediment via different pathways. PBDEs and NBFRs in the hadal sediments were generally transported via the settling of sediment particles of either marine or terrigenous origin whereas in amphipods they accumulated via feeding on animal carrion through the food web. This is the first study reporting on BDE 209 and NBFR contaminations in hadal settings and provide new insight on influencing factors and sources of PBDEs and NBFRs in the deepest oceans.
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Affiliation(s)
- Jingqian Xie
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Organic Geochemistry, Guangdong Key Laboratory of Environment and Resources, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Gaoxin Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qiang Wu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Min Luo
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China.
| | - Duofu Chen
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yu Zhang
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Lisheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Yingming Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Qinghua Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tian Lin
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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25
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Ji B, Qin J, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52087-52106. [PMID: 36826766 DOI: 10.1007/s11356-023-25962-1] [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: 10/09/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.
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Affiliation(s)
- Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xin Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Tian Wang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Guoliang Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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26
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Habibi N, Uddin S, Al-Sarawi H, Aldhameer A, Shajan A, Zakir F, Abdul Razzack N, Alam F. Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome. Microorganisms 2023; 11:microorganisms11020531. [PMID: 36838497 PMCID: PMC9960530 DOI: 10.3390/microorganisms11020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
- Correspondence:
| | - Saif Uddin
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Hanan Al-Sarawi
- Environment Public Authority, Fourth Ring Road, Shuwaikh Industrial 70050, Kuwait
| | - Ahmed Aldhameer
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
| | - Faiz Alam
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait
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Lu S, Wang J, Wang B, Xin M, Lin C, Gu X, Lian M, Li Y. Comprehensive profiling of the distribution, risks and priority of pharmaceuticals and personal care products: A large-scale study from rivers to coastal seas. WATER RESEARCH 2023; 230:119591. [PMID: 36638740 DOI: 10.1016/j.watres.2023.119591] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Pharmaceuticals and personal care products (PPCPs) have captured global concern due to their detrimental effects on aquatic organisms. Thirty PPCPs were analyzed in the water of the Jiaozhou Bay watershed, the Yellow Sea (YS) and the East China Sea (ECS) in China to investigate the distribution and risk of PPCPs from rivers to coastal seas, which are not yet well documented. The results showed the prevalence of the target PPCPs with a downward trend in detection frequencies and total concentrations from rivers (675 ng/L on average) to bay (166 ng/L) and to coastal seas (103 ng/L). Antibiotics and personal care products (PCPs) were dominated by amoxicillin (AMOX) and p-hydroxybenzoic acid, respectively, while the dominant estrogens were inconsistent in different regions. Spatially, the total PPCP concentrations were higher in the ECS than that in the YS due to the larger quantity of sewage flowing into the ECS. Additionally, higher total PPCP concentrations were appeared in the southeastern waters outside the Yangtze estuary and Hangzhou Bay of the ECS. The PPCP mixtures might pose medium to high risk to aquatic organisms in general. The total risk quotient (RQT) of antibiotics and PCPs to algae was higher than that to crustacean and fish, while estrogens may cause the greatest damage to fish. Despite the higher PPCP concentrations in river water than in seawater, the RQT of PPCPs in bay water was generally higher than that in river water, which may be associated with the susceptibility of marine organisms. Furthermore, the high-risk pollutants that need special concern in different regions were clarified, showing that AMOX, 17ß-estradiol, and estriol deserve the highest-priority in rivers, bay, and coastal waters, respectively.
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Affiliation(s)
- Shuang Lu
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Jing Wang
- Beijing Normal University, Beijing 100875, China
| | - Baodong Wang
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Ming Xin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Chunye Lin
- Beijing Normal University, Beijing 100875, China.
| | - Xiang Gu
- Beijing Normal University, Beijing 100875, China
| | - Maoshan Lian
- Beijing Normal University, Beijing 100875, China
| | - Yun Li
- Beijing Normal University, Beijing 100875, China
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28
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Yang F, Wang X, Tian X, Zhang Z, Zhang K, Zhang K. Cow manure simultaneously reshaped antibiotic and metal resistome in the earthworm gut tract by metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159010. [PMID: 36174681 DOI: 10.1016/j.scitotenv.2022.159010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Earthworm conversion is an eco-friendly biological process that converts livestock waste into a benign nutrient-rich organic fertilizer. However, little is known about the impacts of earthworm-converted livestock manure on the antibiotic resistome in the earthworm gut microbiota. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift of antibiotic resistance genes (ARGs) in the earthworm gut-feeding on cow manure (CM)-by metagenomic analysis. The effects of copper (Cu) as a food addictive were also evaluated. CM substantially enriched the antibiotic resistome in the foregut and midgut, while it decreased in the hindgut. A similar trend was observed for metal resistance genes (MRGs). Notably, Cu in the CM had little effect on composition of ARGs and MRGs in earthworm gut. The earthworm gut microbiome altered by CM was responsible for the shift of ARGs and MRGs. In wormcast, Cu (100 and 300 mg/kg) significantly increased the abundance of ARGs and MRGs. Our study provides valuable insight into the response of ARGs and MRGs to CM in earthworm gut, and underscores the need for the judicious use of heavy metals as feed additives in livestock and poultry farming.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xueli Tian
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Zulin Zhang
- The James Hutton Institute, Aberdeen AB158QH, UK
| | - Kai Zhang
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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Distributional Pattern of Bacteria, Protists, and Diatoms in Ocean according to Water Depth in the Northern South China Sea. Microbiol Spectr 2022; 10:e0275921. [PMID: 36222702 PMCID: PMC9769685 DOI: 10.1128/spectrum.02759-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.
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30
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Zhang Y, Zhang B, Ahmed I, Zhang H, He Y. Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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31
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Yang F, Shen S, Gao W, Ma Y, Han B, Ding Y, Wang X, Zhang K. Deciphering discriminative antibiotic resistance genes and pathogens in agricultural soil following chemical and organic fertilizer. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116110. [PMID: 36049303 DOI: 10.1016/j.jenvman.2022.116110] [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: 05/28/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Fertilizers containing rich nutrients can change the profiles of antibiotic resistant pathogens (ARPs) and antibiotic resistance genes (ARGs) in receiving soils; however, the discriminative ARGs and ARPs in agricultural soil following different fertilizer applications remain unknown. Using metagenomic sequencing combined with binning approach, the present study investigated the discriminative ARGs and ARPs under various fertilizer applications (chemical and organic fertilizer) in a 8-year field experiment. VanR, multidrug ARG transporter, vanS, ermA, and arnA were the discriminative ARGs in the chemical fertilizer group, whereas rosB, multidrug transporter, mexW, and aac(3)-I were enhanced in the organic fertilizer group. The metagenomic binning approach revealed that both fertilizer applications caused pathogen proliferation. Chemical fertilizer caused the increase in the pathogenic genus Luteimonas, and organic fertilizer facilitated the proliferation of the pathogenic genera Dokdonella and Pseudomonas. The pathogenic species Pseudomonas_H sp014836765, carrying mexW and multidrug transporter, was enriched only in the organic fertilizer group, indicating that it was a discriminative ARP in the organic fertilizer group. Our results demonstrated that fertilizer application, particularly organic fertilizer application, can facilitate the proliferation of ARGs and ARPs in the receiving soil, posing the risk of the development and spread of soil-borne ARPs.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Wenxuan Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Yingjun Ma
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiaolong Wang
- School of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China.
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32
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Sazykina M, Barabashin T, Konstantinova E, Al-Rammahi AAK, Pavlenko L, Khmelevtsova L, Karchava S, Klimova M, Mkhitaryan I, Khammami M, Sazykin I. Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov. MARINE POLLUTION BULLETIN 2022; 184:114196. [PMID: 36219972 DOI: 10.1016/j.marpolbul.2022.114196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 09/10/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.
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Affiliation(s)
- Marina Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
| | - Timofey Barabashin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation; Azov-Black Sea Branch of Russian Federal Research Institute of Fisheries and Oceanography, 21v Beregovaya St., Rostov-on-Don 344002, Russian Federation
| | | | | | - Liliya Pavlenko
- Azov-Black Sea Branch of Russian Federal Research Institute of Fisheries and Oceanography, 21v Beregovaya St., Rostov-on-Don 344002, Russian Federation
| | - Lyudmila Khmelevtsova
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - Shorena Karchava
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - Maria Klimova
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - Irina Mkhitaryan
- Azov-Black Sea Branch of Russian Federal Research Institute of Fisheries and Oceanography, 21v Beregovaya St., Rostov-on-Don 344002, Russian Federation
| | - Margarita Khammami
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - Ivan Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
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33
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Zhang X, Wu K, Han Z, Chen Z, Liu Z, Sun Z, Shao L, Zhao Z, Zhou L. Microbial diversity and biogeochemical cycling potential in deep-sea sediments associated with seamount, trench, and cold seep ecosystems. Front Microbiol 2022; 13:1029564. [PMID: 36386615 PMCID: PMC9650238 DOI: 10.3389/fmicb.2022.1029564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2023] Open
Abstract
Due to their extreme water depths and unique physicochemical conditions, deep-sea ecosystems develop uncommon microbial communities, which play a vital role in biogeochemical cycling. However, the differences in the compositions and functions of the microbial communities among these different geographic structures, such as seamounts (SM), marine trenches (MT), and cold seeps (CS), are still not fully understood. In the present study, sediments were collected from SM, MT, and CS in the Southwest Pacific Ocean, and the compositions and functions of the microbial communities were investigated by using amplicon sequencing combined with in-depth metagenomics. The results revealed that significantly higher richness levels and diversities of the microbial communities were found in SM sediments, followed by CS, and the lowest richness levels and diversities were found in MT sediments. Acinetobacter was dominant in the CS sediments and was replaced by Halomonas and Pseudomonas in the SM and MT sediments. We demonstrated that the microbes in deep-sea sediments were diverse and were functionally different (e.g., carbon, nitrogen, and sulfur cycling) from each other in the seamount, trench, and cold seep ecosystems. These results improved our understanding of the compositions, diversities and functions of microbial communities in the deep-sea environment.
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Affiliation(s)
- Xiaoyong Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Keyue Wu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Zihui Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhiying Liu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zuwang Sun
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Liyi Shao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Lei Zhou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Wang N, Xue L, Ding G, Han Y, Feng Y, Liu J, Li N, He W. High concentration of ammonia sensitizes the response of microbial electrolysis cells to tetracycline. WATER RESEARCH 2022; 225:119064. [PMID: 36130438 DOI: 10.1016/j.watres.2022.119064] [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] [Received: 06/28/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Microbial electrolysis cell (MEC) is a promising technology for effective energy conversion of wastewater organics to biogas. Yet, in swine wastewater treatment, the complex contaminants including antibiotics may affect MEC performance, while the high ammonia concentration might increase this risk by increasing cell membrane permeability. In this work, the responses of MECs on tetracycline (TC) with low and high ammonia loadings (80 and 1000 mg L-1) were fully investigated. The TC of 0 to 1 mg L-1 slightly improved MEC performance in current production and electrochemical characteristics with low ammonia loading, while TC ≥ 4 mg L-1 started to show negative effects. Generally, the high ammonia loading sensitized MECs to TC concentration, inducing the current and COD removal of MECs to sharply decline with TC ≥ 0.5 mg L-1. The positive effect of high ammonia loading on MEC due to conductivity increase was counteracted with TC ≥ 1 mg L-1. The co-contamination of TC and ammonia significantly decreased the bioactivity and biomass of anode biofilm. Although the high concentration of co-existing TC and ammonia inhibited MEC performance, the reactors still obtained positive energy feedback. The network analyses indicated that the effluent suspension contributed much to antibiotic resistance gene (ARG) transmission, while the microplastics (MPs) in wastewater greatly raised the risks of ARGs spreading. This work systematically examined the synergetic effects of TC and ammonia and the transmission of ARGs in MEC operation, which is conducive to expediting the application of MECs in swine wastewater treatment.
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Affiliation(s)
- Naiyu Wang
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Lefei Xue
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Guofang Ding
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yu Han
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yujie Feng
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
| | - Jia Liu
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Nan Li
- School of Environmental Science and Engineering, Academy of Ecology and Environment, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Weihua He
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73 Huang he Road, Nangang District, Harbin 150090, China.
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Su H, Wu C, Han P, Liu Z, Liang M, Zhang Z, Wang Z, Guo G, He X, Pang J, Wang C, Weng S, He J. The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129543. [PMID: 35870206 DOI: 10.1016/j.jhazmat.2022.129543] [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: 04/27/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The hadal biosphere, the deepest part of the ocean, is known as the least-explored aquatic environment and hosts taxonomically diverse microbial communities. However, the microbiome and its association with antibiotic resistance genes (ARGs) in the hadal ecosystem remain unknown. Here, we profiled the microbiome diversity and ARG occurrence in seawater and sediments of the Yap Trench (YT) using metagenomic sequencing. Within the prokaryote (bacteria and archaea) lineages, the main components of bacteria were Gammaproteobacteria (77.76 %), Firmicutes (8.36 %), and Alphaproteobacteria (2.25 %), whereas the major components of archaea were Nitrososphaeria (6.51 %), Nanoarchaeia (0.42 %), and Thermoplasmata (0.25 %), respectively. Taxonomy of viral contigs showed that the classified viral communities in YT seawater and sediments were dominated by Podoviridae (45.96 %), Siphoviridae (29.41 %), and Myoviridae (24.63 %). A large majority of viral contigs remained uncharacterized and exhibited endemicity. A total of 48 ARGs encoding resistance to 12 antibiotic classes were identified and their hosts were bacteria and viruses. Novel ARG subtypes mexFYTV-1, mexFYTV-2, mexFYTV-3, vanRYTV-1, vanSYTV-1 (carried by unclassified viruses), and bacAYTB-1 (carried by phylum Firmicutes) were detected in seawater samples. Overall, our findings imply that the hadal environment of the YT is a repository of viral and ARG diversity.
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Affiliation(s)
- Hualong Su
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Chengcheng Wu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Peiyun Han
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zixuan Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Mincong Liang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Zheng Zhang
- Baidu International Technology (Shenzhen), Shenzhen 518062, China
| | - Zhike Wang
- Hainan Guodun Information Development, Haikou 570206, China
| | - Guangyu Guo
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Xinyi He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhu Pang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Shaoping Weng
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianguo He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China; State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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36
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Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean. Appl Environ Microbiol 2022; 88:e0057522. [PMID: 35916502 PMCID: PMC9397096 DOI: 10.1128/aem.00575-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.
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Guan Y, Jia J, Fan X, Li K, Wang Z. Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106221. [PMID: 35709638 DOI: 10.1016/j.aquatox.2022.106221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.
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Affiliation(s)
- Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiqi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait. SUSTAINABILITY 2022. [DOI: 10.3390/su14138029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Marine sediments are a sink for antibiotic resistance genes (ARGs) and antibiotic-resistant microbes (ARMs). Wastewater discharge into the aquatic environment is the dominant pathway for pharmaceuticals reaching aquatic organisms. Hence, the characterization of ARGs is a priority research area. This baseline study reports the presence of ARGs in 12 coastal sediment samples covering the urban coastline of Kuwait through whole-genome metagenomic sequencing. The presence of 402 antibiotic resistance genes (ARGs) were recorded in these samples; the most prevalent were patA, adeF, ErmE, ErmF, TaeA, tetX, mphD, bcrC, srmB, mtrD, baeS, Erm30, vanTE, VIM-7, AcrF, ANT4-1a, tet33, adeB, efmA, and rpsL, which showed resistance against 34 drug classes. Maximum resistance was detected against the beta-lactams (cephalosporins and penam), and 46% of genes originated from the phylum Proteobacteria. Low abundances of ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sps., and Escherichia coli) were also recorded. Approximately 42% of ARGs exhibited multiple drug resistance. All the ARGs exhibited spatial variations. The major mode of action was antibiotic efflux, followed by antibiotic inactivation, antibiotic target alteration, antibiotic target protection, and antibiotic target replacement. Our findings supported the occurrence of ARGs in coastal marine sediments and the possibility of their dissemination to surrounding ecosystems.
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A Comprehensive Profile of Antibiotic Resistance Genes in the Water Column of a Shallow-Sea Hydrothermal Vent Ecosystem. SUSTAINABILITY 2022. [DOI: 10.3390/su14031776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance genes (ARGs) became an emerging contaminant, and were found to accumulate in natural and man-made environments. A comprehensive understanding of the diversity and abundance of ARGs in pristine environments is critical for defining the baseline levels of environmental ARGs. However, there is limited information available on the ARG profiles of pristine environments, especially for shallow-sea hydrothermal vents ecosystems. Here, we combined 16S rRNA gene full-length amplicon sequencing and high-throughput quantitative PCR (HT-qPCR) to study the bacterial communities, and ARG abundance and diversity in the shallow-sea hydrothermal vent ecosystem of the Kueishantao Islet. The results of the 16S rRNA gene amplicon sequencing showed that several sulfur-cycling related bacterial genera, including Thiomicrorhabdus, Thioreductor, Sulfurovum, Sulfurimonas and Lebetimonas, dominated in the water column of the shallow-sea system. Temperature was the significant factor shaping the bacterial communities. The results of HT-qPCR analysis showed that the Kueishantao shallow-sea system harbored the lowest diversity (average 10 ARG subtypes) and abundance (average 1.0 × 10−3 copy per bacterial cell) of ARGs compared with other pristine (i.e., Tibet lake sediments, marine water and sediments) and anthropogenic-disturbed (i.e., drinking water reservoirs, urban ponds and wastewater treatment plants) environments. Procrustes analysis demonstrated a concordant pattern between the compositions of bacterial communities and ARGs in the shallow-sea system, while variation partition analysis revealed that the shared effects of physicochemical and bacterial communities explained >80% of the variation in the composition of ARGs. These results suggest that the vent bacterial communities and local environmental factors played an important role in shaping the distribution of the ARG profiles. Our study provides the first comprehensive overview of the background level of ARGs in a shallow-sea hydrothermal vent ecosystem.
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