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Li J, Li L, Li Q, Fang W, Sun Y, Lu Y, Wang J, Zhu Y, Zhang Y. Distribution and relationship of antibiotics, heavy metals and resistance genes in the upstream of Hanjiang River Basin in Shiyan, China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:7115-7130. [PMID: 37453967 DOI: 10.1007/s10653-023-01683-9] [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: 03/28/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The upstream basin of Hanjiang River is an important water source for the middle route of China's South-to-North Water Diversion Project. The quality of water and soil in the Hanjiang River have enormous biological and environmental impacts, and resistant genetic contamination has emerged, but only few studies are concerned the correlation between heavy metals and metal resistance genes (MRGs). In this study, 8 antibiotics and 19 heavy metals were analyzed, the results showed that the highest antibiotic content was tetracycline, with mean concentrations of 43.201 µg/kg and 0.022 µg/L. Mn was the highest heavy metal in soil with a content of 1408.284 µg/kg, and in water was Zn with a content of 10.611 µg/L. We found that the most abundant antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the study area were bacA and arsT genes, coding for resistance mechanisms to bacitracin and arsenic, respectively. The data showed that heavy metals had a greater impact on antibiotic resistance genes than antibiotics, and the correlation between resistance genes was significantly positive. This work expands our understanding of the correlations of antibiotics, heavy metals, and resistance genes in the Hanjiang River, indicating that more attention should be paid to the effects of resistance genes and the quality of water.
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Affiliation(s)
- Jing Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Lijuan Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Qin Li
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Wen Fang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yonghao Sun
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yu Lu
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Jing Wang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China
| | - Yanrong Zhu
- Hanjiang Bureau of Hydrology and Water Resources Survey, Bureau of Hydrology, Changjiang Water Resources Commission, Xiangyang, 441022, People's Republic of China
| | - Yao Zhang
- Center for Environment and Health in Water Source Area of South-to-North Water Diversion, School of Public Health, Hubei University of Medicine, Shiyan, 442000, People's Republic of China.
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Colin Y, Arcanjo C, Da Costa C, Vivant AL, Trémolet G, Giusti-Petrucciani N, Duflot A, Forget-Leray J, Berthe T, Boulangé-Lecomte C. Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 259:106546. [PMID: 37120957 DOI: 10.1016/j.aquatox.2023.106546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. Of particular importance is that trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L-1) over a 72-hour time period. The copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis and the alteration of its microbiota. Unexpectedly, very few genes were differentially expressed in the copper-treated copepods compared to the controls for both male and female samples, while a clear dichotomy between sex was highlighted with 80% of the genes showing sex-biased expression. In contrast, copper increased the taxonomic diversity of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated the phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in the copper-treated copepods coincided with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, Alkanindiges, Colwellia) and a higher relative abundance of the copAox gene encoding a periplasmic inducible multi-copper oxidase. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines the need to consider the microbial component during evaluation of the vulnerability of zooplankton to metallic stress.
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Affiliation(s)
- Yannick Colin
- Univ Rouen Normandie, UNICAEN, CNRS, M2C UMR 6143, F-76000 Rouen, France; Sorbonne Université, CNRS, EPHE, UMR METIS, F-75005, Paris, France.
| | - Caroline Arcanjo
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
| | - Claire Da Costa
- Univ Rouen Normandie, UNICAEN, CNRS, M2C UMR 6143, F-76000 Rouen, France
| | - Anne-Laure Vivant
- Univ Rouen Normandie, UNICAEN, CNRS, M2C UMR 6143, F-76000 Rouen, France
| | - Gauthier Trémolet
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
| | - Nathalie Giusti-Petrucciani
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
| | - Aurélie Duflot
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
| | - Joëlle Forget-Leray
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
| | - Thierry Berthe
- Univ Rouen Normandie, UNICAEN, CNRS, M2C UMR 6143, F-76000 Rouen, France; Sorbonne Université, CNRS, EPHE, UMR METIS, F-75005, Paris, France
| | - Céline Boulangé-Lecomte
- Université Le Havre Normandie, Normandie Univ, FR CNRS 3730 SCALE, UMR-I 02 SEBIO, Le Havre, F-76600 Le Havre, France
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Zhu J, Huang Q, Peng X, Zhou X, Gao S, Li Y, Luo X, Zhao Y, Rensing C, Su J, Cai P, Liu Y, Chen W, Hao X, Huang Q. MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10656-10667. [PMID: 35876052 DOI: 10.1021/acs.est.2c00488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial metal detoxification mechanisms have been well studied for centuries in pure culture systems. However, profiling metal resistance determinants at the community level is still a challenge due to the lack of comprehensive and reliable quantification tools. Here, a novel high-throughput quantitative polymerase chain reaction (HT-qPCR) chip, termed the metal resistance gene (MRG) chip, has been developed for the quantification of genes involved in the homeostasis of 9 metals. The MRG chip contains 77 newly designed degenerate primer sets and 9 published primer sets covering 56 metal resistance genes. Computational evaluation of the taxonomic coverage indicated that the MRG chip had a broad coverage matching 2 kingdoms, 29 phyla, 64 classes, 130 orders, 226 families, and 382 genera. Temperature gradient PCR and HT-qPCR verified that 57 °C was the optimal annealing temperature, with amplification efficiencies of over 94% primer sets achieving 80-110%, with R2 > 0.993. Both computational evaluation and the melting curve analysis of HT-qPCR validated a high specificity. The MRG chip has been successfully applied to characterize the distribution of diverse metal resistance determinants in natural and human-related environments, confirming its wide scope of application. Collectively, the MRG chip is a powerful and efficient high-throughput quantification tool for exploring the microbial metal resistome.
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Affiliation(s)
- Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiong Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyi Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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Hao X, Zhu J, Rensing C, Liu Y, Gao S, Chen W, Huang Q, Liu YR. Recent advances in exploring the heavy metal(loid) resistant microbiome. Comput Struct Biotechnol J 2020; 19:94-109. [PMID: 33425244 PMCID: PMC7771044 DOI: 10.1016/j.csbj.2020.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.
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Affiliation(s)
- Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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5
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Wang Q, Liu L, Hou Z, Wang L, Ma D, Yang G, Guo S, Luo J, Qi L, Luo Y. Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137055. [PMID: 32065888 DOI: 10.1016/j.scitotenv.2020.137055] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/08/2020] [Accepted: 01/31/2020] [Indexed: 05/19/2023]
Abstract
Recent studies have consistently demonstrated increasing abundances of antibiotic resistance genes (ARGs) in the absence of antibiotic use. There is a large amount of quantitative data that has correlated the elevated ARGs levels with the concentrations of heavy metals in environments with anthropogenic impact. However, the mechanisms by which heavy metals facilitate the proliferation and horizontal gene transfer of ARGs among environmental bacteria were still unknown. This study validated effects of four typical heavy metals (Cu, Cd, Pb, Zn) on the plasmid RP4 mediated conjugative transfer of ARGs in freshwater microcosms. The results suggested that the typical heavy metals including Cu, Pb and Zn would promote conjugative transfer of the plasmid RP4, and Cu (5.0 μg/L) had the greatest ability to increase conjugative transfer by 16-fold higher than the control groups. In conjugative transfer microcosms, the species of each cultivable transconjugant were isolated, and their minimum inhibitory concentrations (MICs) were assessed via antibiotic susceptibility testing. The mechanism of the increased conjugative transfer of Cu was that Cu induced cell damage and the reduced conjugative transfer of Cd was that Cd increased the content of extracellular polymers substances (EPS). This study confirms that heavy metal Cu facilitates the conjugative transfer of environmental-mediated plasmid RP4 by cell damage effect, therefore accelerating the transmission and proliferation of ARGs.
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Affiliation(s)
- Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Lei Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zelin Hou
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Litao Wang
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Dan Ma
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Guang Yang
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Shaoyue Guo
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Jinghui Luo
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Liying Qi
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China.
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Ouyang W, Gao B, Cheng H, Zhang L, Wang Y, Lin C, Chen J. Airborne bacterial communities and antibiotic resistance gene dynamics in PM 2.5 during rainfall. ENVIRONMENT INTERNATIONAL 2020; 134:105318. [PMID: 31726367 DOI: 10.1016/j.envint.2019.105318] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
The biotoxicity and public health effects of airborne bacteria and antibiotic resistance genes (ARGs) in fine particulate matter (PM2.5) are being increasingly recognized. The characteristics of bacterial community composition and ARGs in PM2.5 under different rainfall conditions were studied based on the on-site synchronous measurements in downtown Beijing. Marked differences were evident in the bacterial community characteristics of PM2.5 before, during, and after rain events (p < 0.05). The rain intensities affected the bacterial community abundance in PM2.5 and heavy rain had greater washing effects. The Proteobacteria (phylum level), α-Proteobacteria (class level), Pseudomonadales (order level), Pseudomonadaceae (family level), and Cyanobacteria (genus level) were the dominant bacterial taxa associated with PM2.5 in Beijing during rain events. However, the bacteria at each level that displayed the biggest percentage variance was not the dominant type under different rain intensities. The ermB, tetW, and mphE genes were the primary ARGs, with abundances of 18 to 30 copies/m3, which was a relatively smaller value than other observations. Real-time monitoring of the meteorological condition of rain events and physicochemical properties of PM2.5 were used to identify the main factors during rainfall. The bacterial community was sensitive to the ionic and metal element components of PM2.5 during rainfall. The abundance of ARGs was closely correlated with some groups of the bacterial community, which were also close to the initial value before the rain. Statistical analysis demonstrated that temperature, relative humidity, and duration of rain were the primary meteorological factors for the biological characteristics. The ionic species, rather than metal elements, in PM2.5 were the sensitive factors for the bacteria community and ARGs, which varied at the phylum, class, order, family, and genus levels. The observations provide insights for the biological risk assessment in an urban rainfall water and the potential health impact on citizens.
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Affiliation(s)
- Wei Ouyang
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China.
| | - Bing Gao
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Hongguang Cheng
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Lei Zhang
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Yidi Wang
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Chunye Lin
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China
| | - Jing Chen
- School of Environment, State Key Laboratory of Water Environment Simulation, Beijing Normal University, Beijing 100875, China; Center of Atmospheric Environmental Studies, Beijing Normal University, Beijing 100875, China
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Besaury L, Pawlak B, Quillet L. Expression of copper-resistance genes in microbial communities under copper stress and oxic/anoxic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4013-4023. [PMID: 25009094 DOI: 10.1007/s11356-014-3254-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/24/2014] [Indexed: 06/03/2023]
Abstract
Microorganisms have developed copper-resistance mechanisms in order to survive in contaminated environments. The abundance and expression of the copper-resistance genes cusA and copA, encoding respectively for a Resistance Cell Nodulation protein and for a P-type ATP-ase pump, was assessed along a gradient of copper concentration in microcosms prepared from Seine estuary mudflat sediment. We demonstrated that the abundance of copA and cusA genes decreased with the increase of copper concentration and that cusA gene was up to ten times higher than the copA gene. Only the copA gene was expressed in both oxic and anoxic conditions. The abundance and activity of the microbial community remained constant whatever the concentrations of copper along the gradient. The molecular phylogeny of the two copper-resistance genes was studied and revealed that the increase of copper increased the diversity of copA and cusA gene sequences.
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Affiliation(s)
- Ludovic Besaury
- Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Bâtiment IRESE B, 2ème étage, UFR des Sciences, Université de Rouen, 76821, Mont Saint Aignan, France.
| | - Barbara Pawlak
- Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Bâtiment IRESE B, 2ème étage, UFR des Sciences, Université de Rouen, 76821, Mont Saint Aignan, France
| | - Laurent Quillet
- Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Bâtiment IRESE B, 2ème étage, UFR des Sciences, Université de Rouen, 76821, Mont Saint Aignan, France
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8
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Choudhary S, Sar P. Real-time PCR based analysis of metal resistance genes in metal resistant Pseudomonas aeruginosa strain J007. J Basic Microbiol 2015; 56:688-97. [PMID: 26662317 DOI: 10.1002/jobm.201500364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/11/2015] [Indexed: 11/09/2022]
Abstract
A uranium (U)-resistant and -accumulating Pseudomonas aeruginosa strain was characterized to assess the response of toxic metals toward its growth and expression of metal resistance determinants. The bacterium showed MIC (minimum inhibitory concentration) values of 6, 3, and 2 mM for Zn, Cu, and Cd, respectively; with resistance phenotype conferred by periplasmic Cu sequestering copA and RND type heavy metal efflux czcA genes. Real-time PCR-based expression analysis revealed significant upregulation of both these genes upon exposure to low concentrations of metals for short duration, whereas the global stress response gene sodA encoding superoxide dismutase enzyme was upregulated only at higher metal concentrations or longer exposure time. It could also be inferred that copA and czcA are involved in providing resistance only at low metal concentrations, whereas involvement of "global stress response" phenomenon (expression of sodA) at higher metal concentration or increased exposure was evident. This study provides significant understanding of the adaptive response of bacteria surviving in metal and radionuclide contaminated environments along with the development of real-time PCR-based quantification method of using metal resistance genes as biomarker for monitoring relevant bacteria in such habitats.
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Affiliation(s)
- Sangeeta Choudhary
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
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Becerra-Castro C, Machado RA, Vaz-Moreira I, Manaia CM. Assessment of copper and zinc salts as selectors of antibiotic resistance in Gram-negative bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 530-531:367-372. [PMID: 26057541 DOI: 10.1016/j.scitotenv.2015.05.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 06/04/2023]
Abstract
Some metals are nowadays considered environmental pollutants. Although some, like Cu and Zn, are essential for microorganisms, at high concentrations they can be toxic or exert selective pressures on bacteria. This study aimed to assess the potential of Cu or Zn as selectors of specific bacterial populations thriving in wastewater. Populations of Escherichia coli recovered on metal-free and metal-supplemented culture medium were compared based on antibiotic resistance phenotype and other traits. In addition, the bacterial groups enriched after successive transfers in metal-supplemented culture medium were identified. At a concentration of 1mM, Zn produced a stronger inhibitory effect than Cu on the culturability of Enterobacteriaceae. It was suggested that Zn selected populations with increased resistance prevalence to sulfamethoxazole or ciprofloxacin. In non-selective culture media, Zn or Cu selected for mono-species populations of ubiquitous Betaproteobacteria and Flavobacteriia, such as Ralstonia pickettii or Elizabethkingia anophelis, yielding multidrug resistance profiles including resistance against carbapenems and third generation cephalosporins, confirming the potential of Cu or Zn as selectors of antibiotic resistant bacteria.
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Affiliation(s)
- Cristina Becerra-Castro
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Rita A Machado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.
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10
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Isolation and Characterization of Multi-Metal-Resistant Halomonas sp. MG from Tamil Nadu Magnesite Ore Soil in India. Curr Microbiol 2015; 71:618-23. [DOI: 10.1007/s00284-015-0897-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/23/2015] [Indexed: 01/30/2023]
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11
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Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes. Sci Rep 2015; 5:13258. [PMID: 26286020 PMCID: PMC4541151 DOI: 10.1038/srep13258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/16/2015] [Indexed: 11/17/2022] Open
Abstract
Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.
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12
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Sharma S, Vakhlu J. Metagenomics as advanced screening methods for novel microbial metabolites. Microb Biotechnol 2014. [DOI: 10.1201/b17587-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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13
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Kaci A, Petit F, Lesueur P, Boust D, Vrel A, Berthe T. Distinct diversity of the czcA gene in two sedimentary horizons from a contaminated estuarine core. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:10787-10802. [PMID: 24894751 DOI: 10.1007/s11356-014-3029-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
In estuarine ecosystems, trace metals are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediments accumulate and are then transformed by diagenetic processes, recording the history of the estuary's chemical contamination. In such a specific environment, we investigated to what extent a chronic exposure to contaminants could affect metal-resistant sedimentary bacteria in subsurface sediments. The occurrence and diversity of cadmium resistance genes (cadA, czcA) was investigated in 5- and 33-year-old sediments from a highly contaminated estuary (Seine France). Primers were designed to detect a 252-bp fragment of the czcA gene, specifically targeting a transmembrane helice domain (TMH IV) involved in the proton substrate antiport of this efflux pump. Although the cadA gene was not detected, the highest diversity of the sequence of the czcA gene was observed in the 5-year-old sediment. According to the percentage of identity at the amino acid level, the closest CzcA relatives were identified among Proteobacteria (α, β, γ, and δ), Verrucomicrobia, Nitrospirae, and Bacteroidetes. The most abundant sequences were affiliated with Stenotrophomonas. In contrast, in the 33-year-old sediment, CzcA sequences were mainly related to Rhodanobacter thiooxydans and Stenotrophomonas, suggesting a shaping of the metal-resistant microbial communities over time by both diagenetic processes and trace metal contamination.
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Affiliation(s)
- Assia Kaci
- CNRS, UMR 6143 M2C, Universités de Rouen-Caen, Normandie Université, 76821, Mont-Saint-Aignan, Cedex, France
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14
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Puopolo G, Giovannini O, Pertot I. Lysobacter capsici AZ78 can be combined with copper to effectively control Plasmopara viticola on grapevine. Microbiol Res 2014; 169:633-42. [DOI: 10.1016/j.micres.2013.09.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/16/2013] [Accepted: 09/21/2013] [Indexed: 11/15/2022]
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15
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Liu J, Hua ZS, Chen LX, Kuang JL, Li SJ, Shu WS, Huang LN. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl Environ Microbiol 2014; 80:3677-86. [PMID: 24727268 PMCID: PMC4054149 DOI: 10.1128/aem.00294-14] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/02/2014] [Indexed: 11/20/2022] Open
Abstract
Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.
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16
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Besaury L, Ghiglione JF, Quillet L. Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:230-242. [PMID: 24072336 DOI: 10.1007/s10126-013-9542-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 09/10/2013] [Indexed: 06/02/2023]
Abstract
We analyzed the impact of copper mine tailing discharges on benthic Archaea and Bacteria around the city of Chanaral in northern Chile. Quantitative PCR (Q-PCR) showed that the bacteria dominated the prokaryotic community at both sites, but only the bacteria showed a decrease in abundance in the copper-contaminated site. Q-PCR on reverse transcripts indicated a higher activity of both bacterial and archaeal communities in the contaminated site, suggesting an adaptation of the two communities to copper. This hypothesis was reinforced by the concomitant augmentation of the copper-resistant copA gene coding for a P-type ATP-ase pump in the contaminated site. The metabolically active bacterial community of the contaminated site was dominated by Gammaproteobacteria related to Ectothiorhodospiraceae and Chromatiaceae and by Alphaproteobacteria phylum related to Rhodobacteraceae. The metabolically active archaeal community was dominated by one lineage belonging to unclassified Euryarchaeota and to methanogenic Archaea.
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Affiliation(s)
- Ludovic Besaury
- Faculté des Sciences, CNRS UMR 6143-M2C, Groupe de Microbiologie, Université de Rouen, Place Emile Blondel, 76821, Mont Saint Aignan Cedex, France,
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17
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Besaury L, Bodilis J, Delgas F, Andrade S, De la Iglesia R, Ouddane B, Quillet L. Abundance and diversity of copper resistance genes cusA and copA in microbial communities in relation to the impact of copper on Chilean marine sediments. MARINE POLLUTION BULLETIN 2013; 67:16-25. [PMID: 23298430 DOI: 10.1016/j.marpolbul.2012.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/01/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Microorganisms have developed copper-resistance mechanisms in order to survive in contaminated environments. The abundance of the copper-resistance genes cusA and copA, encoding respectively for a Resistance Cell Nodulation protein and for a P-type ATP-ase pump, was assessed in copper and non-copper-impacted Chilean marine sediment cores by the use of molecular tools. We demonstrated that number of copA and cusA genes per bacterial cell was higher in the contaminated sediment, and that copA gene was more abundant than cusA gene in the impacted sediment. The molecular phylogeny of the two copper-resistance genes was studied and reveals an impact of copper on the genetic composition of copA and cusA genes.
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Affiliation(s)
- Ludovic Besaury
- Faculté des Sciences, Université de Rouen, CNRS UMR 6143-M2C, Groupe de Microbiologie, Place Emile Blondel, 76821 Mont Saint Aignan Cedex, France.
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18
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Besaury L, Marty F, Buquet S, Mesnage V, Muyzer G, Quillet L. Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments. MICROBIAL ECOLOGY 2013; 65:311-324. [PMID: 22976340 DOI: 10.1007/s00248-012-0120-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.
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Affiliation(s)
- Ludovic Besaury
- UMR CNRS 6143 M2C-groupe Microbiologie, Université de Rouen, Mont Saint Aignan, Rouen, France.
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Abstract
As a trace element copper has an important role in cellular function like many other transition metals. Its ability to undergo redox changes [Cu(I) ↔ Cu(II)] makes copper an ideal cofactor in enzymes catalyzing electron transfers. However, this redox change makes copper dangerous for a cell since it is able to be involved in Fenton-like reactions creating reactive oxygen species (ROS). Cu(I) also is a strong soft metal and can attack and destroy iron-sulfur clusters thereby releasing iron which can in turn cause oxidative stress. Therefore, copper homeostasis has to be highly balanced to ensure proper cellular function while avoiding cell damage.Throughout evolution bacteria and archaea have developed a highly regulated balance in copper metabolism. While for many prokaryotes copper uptake seems to be unspecific, others have developed highly sophisticated uptake mechanisms to ensure the availability of sufficient amounts of copper. Within the cytoplasm copper is sequestered by various proteins and molecules, including specific copper chaperones, to prevent cellular damage. Copper-containing proteins are usually located in the cytoplasmic membrane with the catalytic domain facing the periplasm, in the periplasm of Gram-negative bacteria, or they are secreted, limiting the necessity of copper to accumulate in the cytoplasm. To prevent cellular damage due to excess copper, bacteria and archaea have developed various copper detoxification strategies. In this chapter we attempt to give an overview of the mechanisms employed by bacteria and archaea to handle copper and the importance of the metal for cellular function as well as in the global nutrient cycle.
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Affiliation(s)
- Christopher Rensing
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1870, Frederiksberg C, Denmark
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Iqbal HA, Feng Z, Brady SF. Biocatalysts and small molecule products from metagenomic studies. Curr Opin Chem Biol 2012; 16:109-16. [PMID: 22455793 DOI: 10.1016/j.cbpa.2012.02.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 11/30/2022]
Abstract
The vast majority of bacteria present in environmental samples have never been cultured and therefore have not been exploited for the ability to produce useful biocatalysts or collections of biocatalysts generating interesting small molecules. Metagenomic libraries constructed using DNA extracted directly from natural bacterial communities offer access to the genetic information present in the genomes of these as yet uncultured bacteria. This review highlights recent efforts to recover both discrete enzymes and small molecules from metagenomic libraries.
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Affiliation(s)
- Hala A Iqbal
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
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De la Iglesia R, Valenzuela-Heredia D, Andrade S, Correa J, González B. Composition dynamics of epilithic intertidal bacterial communities exposed to high copper levels. FEMS Microbiol Ecol 2011; 79:720-7. [DOI: 10.1111/j.1574-6941.2011.01254.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 09/27/2011] [Accepted: 11/06/2011] [Indexed: 11/26/2022] Open
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