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Guo X, Qi Z, Li J, Tong H, Ren N, You S. Overlooked volcanic effect during transmission of antibiotic resistance genes induced by copper and zinc. CHEMOSPHERE 2024; 362:142713. [PMID: 38944351 DOI: 10.1016/j.chemosphere.2024.142713] [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: 04/24/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Adding heavy metals such as copper and zinc to animal feeds is common practice to promote growth, but meanwhile has side consequence of enhancing spread of antibiotic resistance genes (ARGs) in soil. This presents a global challenge to food security and human health. We in this study investigated the transmission of typical ARGs, i. e. β-lactamase genes (β-RGs), in dairy farm environments where dietary Cu and Zn were present in a wide range of concentration. The β-RGs were demonstrated to be highly prevalent across environmental media, with a relative abundance of 94.55%, dominated by mechanisms of antibiotic deactivation (93.75%) and cellular protection (6.25%). More importantly, we first found the transmission of ARGs to be highly dependent on the overlooked volcanic effect, i. e. low-concentration Cu (12-22 mg/kg) and Zn (45-80 mg/kg) acted as micronutrients necessary for microbial growth but facilitated ARGs transfer, whereas higher-concentration Cu (22-39 mg/kg) and Zn (80-153 mg/kg) became toxic to microbial communities and gene expression patterns. Notably, the specific microbial phyla Proteobacteria (2.28-82.94%), Bacteroidetes (0.02-56.48%) and Actinobacteria (1.62-12.92%) exhibited resistance at low concentration of Cu and Zn, which enhanced the transmission of β-RGs. However, this process was inhibited at higher concentration due to inactivation of microbes by Cu and Zn. The increase in resistance was first observed in class Gammaproteobacteria (2.02-88.51%) and Alphaproteobacteria (0.68-10.1%) with increased Cu and Zn concentration. This resulted in heightened transfer of ARGs by tnpA-07 (80.35%) due to protection of thicker cell membrane by chelation with Cu and Zn. This study not only offers mechanistic insights into the volcanic effect of dietary metals on dissemination of ARGs, but also has important implications for safe management of agricultural settings.
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Affiliation(s)
- Xiaorui Guo
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China; School of Food Engineering, Harbin University of Commerce, Harbin, 150028, PR China
| | - Zheng Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China.
| | - Junsheng Li
- School of Food Engineering, Harbin University of Commerce, Harbin, 150028, PR China
| | - Hailong Tong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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Liang H, Huang J, Xia Y, Yang Y, Yu Y, Zhou K, Lin L, Li X, Li B. Spatial distribution and assembly processes of bacterial communities in riverine and coastal ecosystems of a rapidly urbanizing megacity in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173298. [PMID: 38761945 DOI: 10.1016/j.scitotenv.2024.173298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Rapid urbanization has precipitated significant anthropogenic pollution (nutrients and pathogens) in urban rivers and their receiving systems, which consequentially disrupted the compositions and assembly of bacterial community within these ecosystems. However, there remains scarce information regarding the composition and assembly of both planktonic and benthic bacterial communities as well as pathogen distribution in such environments. In this study, full-length 16S rRNA gene sequencing was conducted to investigate the bacterial community composition, interactions, and assembly processes as well as the distribution of potential pathogens along a riverine-coastal continuum in Shenzhen megacity, China. The results indicated that both riverine and coastal bacterial communities were predominantly composed of Gammaproteobacteria (24.8 ± 12.6 %), Alphaproteobacteria (16.1 ± 9.8 %), and Bacteroidota (14.3 ± 8.6 %), while sedimentary bacterial communities exhibited significantly higher diversity compared to their planktonic counterparts. Bacterial community patterns exhibited significant divergences across different habitats, and a significant distance-decay relationship of bacterial community similarity was particularly observed within the urban river ecosystem. Moreover, the urban river ecosystem displayed a more complex bacterial co-occurrence network than the coastal ecosystem, and a low ratio of negative:positive cohesion suggested the inherent instability of these networks. Homogeneous selection and dispersal limitation emerged as the predominant influences on planktonic and sedimentary bacterial communities, respectively. Pathogenic genera such as Vibrio, Bacteroides, and Acinetobacter, known for their roles in foodborne diseases or wound infection, were also identified. Collectively, these findings provided critical insights into bacterial community dynamics and their implications for ecosystem management and pathogen risk control in riverine and coastal environments impacted by rapid urbanization.
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Affiliation(s)
- Hebin Liang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Huang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Yang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
| | - Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Disease, Shenzhen People's Hospital (the First Affiliated Hospital, Southern University of Science and Technology; the Second Clinical Medical College, Jinan University), Shenzhen 518020, China
| | - Lin Lin
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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Fan Y, Chen K, Dai Z, Peng J, Wang F, Liu H, Xu W, Huang Q, Yang S, Cao W. Land use/cover drive functional patterns of bacterial communities in sediments of a subtropical river, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174564. [PMID: 38972401 DOI: 10.1016/j.scitotenv.2024.174564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
The bacterial community in sediment serves as an important indicator for assessing the environmental health of river ecosystems. However, the response of bacterial community structure and function in river basin sediment to different land use/cover changes has not been widely studied. To characterize changes in the structure, composition, and function of bacterial communities under different types of land use/cover, we studied the bacterial communities and physicochemical properties of the surface sediments of rivers. Surface sediment in cropland and built-up areas was moderately polluted with cadmium and had high nitrogen and phosphorus levels, which disrupted the stability of bacterial communities. Significant differences in the α-diversity of bacterial communities were observed among different types of land use/cover. Bacterial α-diversity and energy sources were greater in woodlands than in cropland and built-up areas. The functional patterns of bacterial communities were shown that phosphorus levels and abundances of pathogenic bacteria and parasites were higher in cropland than in the other land use/cover types; Urban activities have resulted in the loss of the denitrification function and the accumulation of nitrogen in built-up areas, and bacteria in forested and agricultural areas play an important role in nitrogen degradation. Differences in heavy metal and nutrient inputs driven by land use/cover result in variation in the composition, structure, and function of bacterial communities.
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Affiliation(s)
- Yifei Fan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Kan Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Zetao Dai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiarui Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Feifei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Huibo Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenfeng Xu
- Fujian Xiamen Environmental Monitoring Central Station, Xing'lin South Road, Xiamen, Fujian 361102, China
| | - Quanjia Huang
- Xiamen Environmental Monitoring Station, Xiamen, Fujian 361102, China
| | - Shengchang Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenzhi Cao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.
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Liu X, Zhang L, Wang Y, Hu S, Zhang J, Huang X, Li R, Hu Y, Yao H, Wang Z. Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems. iScience 2024; 27:110053. [PMID: 38947525 PMCID: PMC11214296 DOI: 10.1016/j.isci.2024.110053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/02/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.
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Affiliation(s)
- Xi Liu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, 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, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingcai Wang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Sheng Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Jing Zhang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Xiaolong Huang
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Ruiwen Li
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Yuxin Hu
- Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecological Environment, Wuhan 430010, Hubei, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, Hubei, 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, Hubei, China
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Yadav R, Dharne M. Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:18422-18434. [PMID: 38367110 DOI: 10.1007/s11356-024-32373-3] [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: 10/12/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024]
Abstract
Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.
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Affiliation(s)
- Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Zhang Y, Wang M, Cheng W, Huang C, Ren J, Zhai H, Niu L. Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes. MICROBIAL ECOLOGY 2023; 86:2424-2435. [PMID: 37272971 DOI: 10.1007/s00248-023-02249-z] [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: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.
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Affiliation(s)
- Yutong Zhang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Min Wang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China.
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China.
| | - Wen Cheng
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China.
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China.
| | - Chen Huang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Jiehui Ren
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Hongqin Zhai
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Li Niu
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
- Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
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Ma X, Suo T, Zhao F, Shang Z, Chen Y, Wang P, Li B. Integrating CRISPR/Cas12a with strand displacement amplification for the ultrasensitive aptasensing of cadmium(II). Anal Bioanal Chem 2023; 415:2281-2289. [PMID: 36952025 DOI: 10.1007/s00216-023-04650-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/26/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
Cadmium ion (Cd(II)) is a pernicious environmental pollutant that has been shown to contaminate agricultural lands, accumulate through the food chain, and seriously threaten human health. At present, Cd(II) monitoring is dependent on centralized instruments, necessitating the development of rapid and on-site detection platforms. Against this backdrop, the present study reports on the development of a fluorometric aptasensor designed to target Cd(II), which is achieved through the integration of strand displacement amplification (SDA) and CRISPR/Cas12a. In the absence of Cd(II), the aptamer initiates SDA, resulting in the generation of a profusion of ssDNA that activates Cas12a, leading to a substantial increase in fluorescence output. Conversely, the presence of Cd(II) curtails the SDA efficiency, culminating in a significant reduction in fluorescence output. The proposed approach has been demonstrated to enable the selective detection of Cd(II) at concentrations of 60 pM, with the performance of the aptasensor validated in real water and rice samples. The proposed platform based on aptamer-target interaction holds immense promise as a signal-amplified and precise method for the detection of Cd(II) and has the potential to transform current hazard detection practices in food samples.
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Affiliation(s)
- Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing, 100101, China
| | - Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
- Nanjing Jiangbei New Area Biopharmaceutical Public Platform Co., Ltd., Nanjing, 211899, China
| | - Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Zhaoyang Shang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, 211166, China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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