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Utzman PH, Mays VP, Miller BC, Fairbanks MC, Brazelton WJ, Horvath MP. Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. PLoS One 2024; 19:e0284642. [PMID: 38718041 PMCID: PMC11078426 DOI: 10.1371/journal.pone.0284642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
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Affiliation(s)
- Payton H. Utzman
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Vincent P. Mays
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary C. Fairbanks
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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Bring Horvath ER, Brazelton WJ, Kim MC, Cullum R, Mulvey MA, Fenical W, Winter JM. Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment. ISME COMMUNICATIONS 2024; 4:ycae029. [PMID: 38524762 PMCID: PMC10960970 DOI: 10.1093/ismeco/ycae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/20/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.
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Affiliation(s)
- Elijah R Bring Horvath
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, United States
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, United States
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - William J Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, United States
| | - Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, CA 92093, United States
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, CA 92093, United States
| | - Matthew A Mulvey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, United States
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, CA 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, CA 92093, United States
- Moores Comprehensive Cancer Center, University of California at San Diego, CA 92037, United States
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, United States
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3
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Bring Horvath ER, Brazelton WJ, Kim MC, Cullum R, Mulvey MA, Fenical W, Winter JM. Bacterial Diversity and Chemical Ecology of Natural Product-Producing Bacteria from Great Salt Lake Sediment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.565188. [PMID: 37986792 PMCID: PMC10659378 DOI: 10.1101/2023.11.07.565188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the United States. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5-28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalogue bacteria found in GSL, the Lake's microbiome is largely unexplored, and little-to-no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of a new Saccharomonospora species, and provide the first survey of the natural product potential of GSL bacteria.
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Affiliation(s)
- Elijah R Bring Horvath
- Department of Pharmacology and Toxicology, Department of Medicinal Chemistry, University of Utah, Salt Lake City, United States
| | - William J Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, United States
| | - Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, United States
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, United States
| | - Matthew A Mulvey
- School of Biological Sciences and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, and Moores Comprehensive Cancer Center, University of California at San Diego, San Diego, United States
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, United States
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Zou Y, Xiao Z, Wang L, Wang Y, Yin H, Li Y. Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165441. [PMID: 37437635 DOI: 10.1016/j.scitotenv.2023.165441] [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: 04/24/2023] [Revised: 07/02/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.
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Affiliation(s)
- Yina Zou
- The National Key Laboratory of Water Disaster Prevention, Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Zijian Xiao
- The National Key Laboratory of Water Disaster Prevention, Dayu College, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yutao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Haojie Yin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
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Sidhu AS, Mikolajczyk FN, Fisher JC. Antimicrobial Resistance Linked to Septic System Contamination in the Indiana Lake Michigan Watershed. Antibiotics (Basel) 2023; 12:antibiotics12030569. [PMID: 36978436 PMCID: PMC10044017 DOI: 10.3390/antibiotics12030569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023] Open
Abstract
Extended-spectrum β-lactamases confer resistance to a variety of β-lactam antimicrobials, and the genes for these enzymes are often found on plasmids that include additional antimicrobial resistance genes (ARG). We surveyed aquatic environments in the Indiana Lake Michigan watershed in proximity to areas with high densities of residential septic systems to determine if human fecal contamination from septic effluent correlated with the presence of antimicrobial resistance genes and phenotypically resistant bacteria. Of the 269 E. coli isolated from environmental samples and one septic source, 97 isolates were resistant to cefotaxime, a third-generation cephalosporin. A subset of those isolates showed phenotypic resistance to other β-lactams, fluoroquinolones, sulfonamides, and tetracyclines. Quantitative PCR was used to quantify human-associated Bacteroides dorei gene copies (Human Bacteroides) from water samples and to identify the presence of ARG harbored on plasmids from E. coli isolates or in environmental DNA. We found a strong correlation between the presence of ARG and human fecal concentrations, which supports our hypothesis that septic effluent is a source of ARG and resistant organisms. The observed plasmid-based resistance adds an additional level of risk, as human-associated bacteria from septic systems may expand the environmental resistome by acting as a reservoir of transmissible resistance genes.
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Custodio M, Peñaloza R, Ordinola-Zapata A, Peralta-Ortiz T, Sánches-Suárez H, Vieyra-Peña E, De la Cruz H, Alvarado-Ibáñez J. Diversity of enterobacterales in sediments of lagoons with fish farming activity and analysis of antibiotic resistance. Toxicol Rep 2023; 10:235-244. [PMID: 36845256 PMCID: PMC9950807 DOI: 10.1016/j.toxrep.2023.02.002] [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: 12/29/2022] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The use of antibiotics in fish production can induce bacterial populations to develop resistance to multiple antibiotics and transfer antibiotic resistance genes to other bacteria, including clinically relevant bacteria. This study evaluated the diversity of Enterobacterales in sediment from lagoons with fish farming activity and analyzed antibiotic resistance in the central region of Peru. Sediment samples were collected from four fish-active ponds and transported to the laboratory for analysis. Bacterial diversity was analyzed using DNA sequencing and antibiotic resistance was tested using the disk diffusion method. The results showed variability of bacterial diversity in the ponds with fish farming activity. Simpson's index indicated that the Habascocha lagoon is the most diverse in bacterial species of the order Enterobacterales (0.8), but the least dominant. The Shannon-Wiener index revealed that it is the most diverse (2.93) and the Margalef index revealed that species richness in this lagoon is high (5.72). Similarity percentage analysis (SIMPER) allowed the identification of the main Enterobacterales with the highest percentage contribution in the frequencies of individuals. In general, the Enterobacterales species isolated showed multi-resistance to the antibiotics used and Escherichia coli was the most resistant.
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Affiliation(s)
- María Custodio
- Universidad Nacional del Centro del Perú, Facultad de Medicina Humana, Huancayo, Peru,Corresponding author.
| | - Richard Peñaloza
- Universidad Nacional del Centro del Perú, Facultad de Medicina Humana, Huancayo, Peru
| | | | | | | | | | - Heidi De la Cruz
- Universidad Nacional del Centro del Perú, Facultad de Medicina Humana, Huancayo, Peru
| | - Juan Alvarado-Ibáñez
- Universidad Nacional Intercultural “Fabiola Salazar Leguía” de Bagua, Bagua, Peru
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Su Z, Wen D, Gu AZ, Zheng Y, Tang Y, Chen L. Industrial effluents boosted antibiotic resistome risk in coastal environments. ENVIRONMENT INTERNATIONAL 2023; 171:107714. [PMID: 36571993 DOI: 10.1016/j.envint.2022.107714] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/24/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.
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Affiliation(s)
- Zhiguo Su
- School of Environment, Tsinghua University, Beijing 100084, China; College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Yuhan Zheng
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yushi Tang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, NJ 08544, USA
| | - Lyujun Chen
- School of Environment, Tsinghua University, Beijing 100084, China
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Abstract
Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth's mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.
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Ferreira C, Abreu-Silva J, Manaia CM. The balance between treatment efficiency and receptor quality determines wastewater impacts on the dissemination of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128933. [PMID: 35460999 DOI: 10.1016/j.jhazmat.2022.128933] [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: 10/28/2021] [Revised: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 05/09/2023]
Abstract
This study investigated the balance between treatment efficiency and impact caused by urban wastewater treatment plants (UWTPs) on the dissemination of antibiotic resistance. Four full-scale UWTPs (PT1-PT4) and the receiving river were sampled over four campaigns. The 16 S rRNA gene, two mobile genetic elements (MGEs), eight antibiotic resistance genes (ARGs), and culturable bacteria were monitored over different treatment stages and in hospital effluent. The bacterial and antibiotic resistance load was not significantly different in the inflow of the four UWTPs (p > 0.01). Biological treatment promoted ARGs reduction values up to 2.5 log-units/mL, while UV (PT1, PT2) or sand filtration/ozonation (PT3) led to removal values < 0.6 log-units/mL. The final effluent of PT3, with the highest removal rates and significantly lower ARGs abundance, was not significantly different from the receiving water body. Emerging ARGs (e.g., blaVIM, blaOXA-48, and blaKPC) were sporadically detected in the river, although more frequent downstream. Hospital effluent might contribute for the occurrence of some, but not all these ARGs in the river. A major conclusion was that the impact of the UWTPs on the river was not only determined by treatment efficiency and final effluent quality, but also by the background contamination of the river and/or dilution rate.
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Affiliation(s)
- Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Joana Abreu-Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
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Noman E, Al-Gheethi A, Radin Mohamed RMS, Talip B, Al-Sahari M, Al-Shaibani M. Quantitative microbiological risk assessment of complex microbial community in Prawn farm wastewater and applicability of nanoparticles and probiotics for eliminating of antibiotic-resistant bacteria. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126418. [PMID: 34171673 DOI: 10.1016/j.jhazmat.2021.126418] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The current review highlighted the quantitative microbiological risk assessment of Vibrio parahaemolyticus in Prawn farm wastewaters (PFWWs) and the applicability of nanoparticles for eliminating antibiotic-resistant bacteria (ARB). The high availability of the antibiotics in the environment and their transmission into human through the food-chain might cause unknown health effects. The aquaculture environments are considered as a reservoir for the antibiotic resistance genes (ARGs) and contributed effectively in the increasing of ABR. The metagenomic analysis is used to explore ARGs in the non-clinical environment. V. parahaemolyticus is among the pathogenic bacteria which are transmitted through sea food causing human acute gastroenteritis due to available thermostable direct hemolysin (tdh), adhesins, TDH related hemolysin (trh). The inactivation of pathogenic bacteria using nanoparticles act by disturbing the cell membrane, interrupting the transport system, DNA and mitochondria damage, and oxidizing the cellular component by reactive oxygen species (ROS). The chloramphenicol, nitrofurans, and nitroimidazole are among the prohibited drugs in fish and fishery product. The utilization of probiotics is the most effective and safe alternative for antibiotics in Prawn aquaculture. This review will ensure public understanding among the readers on how they can decrease the risk of the antimicrobial resistance distribution in the environment.
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Affiliation(s)
- Efaq Noman
- Department of Applied Microbiology, Faculty of Applied Science, Taiz University, Yemen; Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Higher Education Hub, KM 1, Jalan Panchor, 84000 Panchor, Johor, Malaysia
| | - Adel Al-Gheethi
- Micropollutant Research Centre (MPRC), Faculty of Civil Engineering & Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja, 86400 Batu Pahat, Johor, Malaysia.
| | - Radin Maya Saphira Radin Mohamed
- Micropollutant Research Centre (MPRC), Faculty of Civil Engineering & Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja, 86400 Batu Pahat, Johor, Malaysia
| | - Balkis Talip
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Higher Education Hub, KM 1, Jalan Panchor, 84000 Panchor, Johor, Malaysia
| | - Mohamed Al-Sahari
- Micropollutant Research Centre (MPRC), Faculty of Civil Engineering & Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja, 86400 Batu Pahat, Johor, Malaysia
| | - Muhanna Al-Shaibani
- Micropollutant Research Centre (MPRC), Faculty of Civil Engineering & Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja, 86400 Batu Pahat, Johor, Malaysia
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Hou L, Wang H, Chen Q, Su JQ, Gad M, Li J, Mulla SI, Yu CP, Hu A. Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126083. [PMID: 34000699 DOI: 10.1016/j.jhazmat.2021.126083] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingfu Chen
- Yundang Lake Management Center, Xiamen, Fujian 361004, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Mahmoud Gad
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore 560064, India
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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12
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Thornton CN, Tanner WD, VanDerslice JA, Brazelton WJ. Localized effect of treated wastewater effluent on the resistome of an urban watershed. Gigascience 2020; 9:5992824. [PMID: 33215210 PMCID: PMC7677451 DOI: 10.1093/gigascience/giaa125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/14/2020] [Indexed: 11/14/2022] Open
Abstract
Background Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a river’s complete set of antibiotic resistance genes (the “resistome") is affected by the release of treated effluent into surface waters. Results Here we used high-throughput, deep metagenomic sequencing to investigate the effect of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the river’s resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points was dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds. Conclusions Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect seems to be localized, with little measurable effect in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.
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Affiliation(s)
- Christopher N Thornton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - Windy D Tanner
- Department of Family and Preventive Medicine, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - James A VanDerslice
- Department of Family and Preventive Medicine, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
| | - William J Brazelton
- School of Biological Sciences, University of Utah, 257 South 1400 East, Rm. 201, 84112, Salt Lake City, UT, USA
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