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Liu X, Zhong B, Li N, Wu WM, Wang X, Li X, Yang Z, Mei X, Yi S, He Y. Notable ecological risks of microplastics to Minjiang River ecosystem over headwater to upstream in Eastern Qinghai-Tibetan Plateau. WATER RESEARCH 2025; 274:123137. [PMID: 39813893 DOI: 10.1016/j.watres.2025.123137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 12/27/2024] [Accepted: 01/11/2025] [Indexed: 01/18/2025]
Abstract
Microplastics (MPs) in aquatic environments has been observed globally. However, the ecological risks of MP pollution in riverhead prior to highly urbanized region remain poorly understood. This study investigated MP pollution related to microbiome in sediments, and ecological risks of MPs in riverhead prior to urbanized area over 291 km of Minjiang River (MJR) in Qinghai-Tibetan Plateau (QTP). MPs in river water and sediments were averagely 245±128 items/L and 124±67 items/kg, respectively, over the investigated river range. The MP distribution indicated that MP abundance is low in headwater section and elevated in middle section and down section with increase of urbanized area. The MPs were found mainly in film, fragments, and fiber morphotypes, with size < 500 μm in both river water and sediments. The polymers of MPs were contributed by polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polyvinyl chloride (PVC), and polycarbonate (PC) at 41.7 %, 22.7 %, 17.9 %, 1.8 %, and 1.2 % in river water, and 32.6 %, 15.0 %, 29.3 %, 3.1 %, and 0.8 % in sediments, respectively. Microbiome analyses of sediments revealed that the majority of microorganisms were aerobic bacteria, which contained potential plastic-degrading bacterial genes. Ecological risk assessment indexes of pollution load, polymeric risk assessment and pollution risk indicated that MPs in MJR river water and sediments displayed noticeable pollution levels, i.e., river water exhibited medium to very high pollution risk levels, and sediments showed from low to very high pollution risk levels in riverhead. Monte Carlo simulation revealed that PVC and PC MPs were considered as priority control pollutants although they were not the most abundant polymers identified due to their intrinsic chemical toxicity. Compared with risk levels of global rivers, the results indicate prominent ecological risks caused by MPs in MJR riverhead areas, and thus raise a warning sign.
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Affiliation(s)
- Xin Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bo Zhong
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Naying Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; School of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, William & Cloy Codiga Resource Recovery Research Center, Stanford University, Stanford, California 94305-4020, United States
| | - Xiaofeng Wang
- School of Geography and Tourism, Chongqing Normal University, Chongqing 400047, China
| | - Xianxiang Li
- School of Geography and Tourism, Chongqing Normal University, Chongqing 400047, China
| | - Zao Yang
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xintong Mei
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shaoliang Yi
- International Centre for Integrated Mountain Development, Kathmandu 3226, Nepal
| | - Yixin He
- CAS Key Laboratory of Mountain Ecological Restoration and Bio-resources Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Laloo AE, Gupta A, Verrone V, Dubey RK. Role of Fe and Mn in organo-mineral-microbe interactions: evidence of carbon stabilization and transformation of organic matter leading to carbon greenhouse gas emissions. Lett Appl Microbiol 2025; 78:ovaf044. [PMID: 40118507 DOI: 10.1093/lambio/ovaf044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 03/10/2025] [Accepted: 03/20/2025] [Indexed: 03/23/2025]
Abstract
Up to 90% of organic matter (OM) in soils and sediments are stabilized and protected against microbial decomposition through organo-mineral interactions, formation of soil aggregates, pH, and oxygen availability. In soils and sediment systems, OM is associated with mineral constituents promoting carbon persistence and sequestration of which iron (Fe) and manganese (Mn) are crucial components. Under anoxic condition, microbes couple the decomposition of OM to the oxidative/reductive transformation of Fe/Mn minerals leading to carbon greenhouse gas (C-GHG) emissions (i.e. CH4 and CO2). Although these organo-mineral-microbe interactions have been observed for decades, the bio-geochemical mechanisms governing the switch from OM stability toward OM degradation are not fully understood. Interest in this field have been growing steadily given the interest in global warming caused by OM decomposition leading to C-GHG emissions. This review emphasizes the dual role of Fe/Mn minerals in both OM stability and decomposition. Additionally, we synthesize the conceptual understanding of how Fe/Mn minerals govern OM dynamics and the resultant C-GHG emissions via microbial-mediated carbon transformation. We highlight the need for interdisciplinary research to better understand organo-Fe/Mn mineral-microbial interactions to develop management handles for climate mitigation strategies.
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Affiliation(s)
- Andrew Elohim Laloo
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
- National University of Singapore Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore, 117411, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore, 117411, Singapore
- Department of Biological Science, National University of Singapore, 117558, Singapore
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
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Patel V, Sharma S, Desai C, Kikani B, Madamwar D. Synergistic removal of emerging contaminants using bacterial augmented floating treatment bed system (FTBs) of Typha latifolia and Canna indica for rejuvenation of polluted river water. Front Microbiol 2025; 16:1512992. [PMID: 40104587 PMCID: PMC11919279 DOI: 10.3389/fmicb.2025.1512992] [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: 10/18/2024] [Accepted: 02/05/2025] [Indexed: 03/20/2025] Open
Abstract
Introduction Floating Treatment Bed systems (FTBs) provide an effective approach to remove pollutants from the rivers. These systems consist of aquatic plants anchored on mats, which support the growth of microbial communities. Such a synergy between plants and microbes in FTBs plays a pivotal role to improve efficacy of river restoration strategies. Methodology The effectiveness of the FTBs was evaluated for the rejuvenation of polluted water from the Mini River in Gujarat, India. These systems consisted of wetland plants, either Typha latifolia or Canna indica, which were augmented with the bacterial consortium VP3. Furthermore, the 16S rRNA gene amplicon sequencing approach identified the dominant bacterial communities and relative microbial community shifts within the FTBs. The presence of emerging contaminants, antimicrobial resistance genes, and pathogenic bacterial species in the untreated river water was evaluated, along with their reduction following treatment through FTBs. This analysis yielded important insights into the microbial dynamics governing the reduction of these contaminants. Results and discussion The bacterial augmented FTBs consisting wet plants achieved reduction of 57%, 70%, 74%, and 80% in biochemical oxygen demand (BOD), chemical oxygen demand (COD), total phosphate, and sulfate, respectively. Moreover, the 16S rRNA gene amplicon sequencing identified Proteobacteria as the dominant phylum, with Pseudomonas species and Hydrogenophaga species being the most abundant genera in FTBs containing T. latifolia and C. indica, respectively. The functional gene prediction indicated presence of various xenobiotic degrading genes too. Non-targeted LC-HRMS analysis of treated water demonstrated complete elimination of antibiotic derivatives and dye intermediates, along with the partial removal of pharmaceutical and personal care products (PPCPs) and chemical intermediates. Additionally, the abundance of probable pathogenic bacteria and dominant antibiotic resistance genes was significantly reduced upon treatment. The phytotoxicity analysis of the treated water supported the outcomes. The studies on removal of emerging contaminants in the polluted river ecosystem has been relatively less explored, highlighting novelty and future possible applications of the plant-microbial augmented FTBs in rejuvenation of polluted rivers.
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Affiliation(s)
- Vandan Patel
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Anand, Gujarat, India
| | - Shruti Sharma
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Anand, Gujarat, India
| | - Chirayu Desai
- Department of Environmental Biotechnology, Gujarat Biotechnology University (GBU), Gandhinagar, Gujarat, India
| | - Bhavtosh Kikani
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Anand, Gujarat, India
| | - Datta Madamwar
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Anand, Gujarat, India
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Hao Z, Chen S, Zhang Q, Liu B. From reduction to rebalancing: Insights into the long-term effects of sediment dredging on nitrogen transformations in river ecosystems. WATER RESEARCH 2024; 267:122460. [PMID: 39306929 DOI: 10.1016/j.watres.2024.122460] [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: 02/26/2024] [Revised: 09/10/2024] [Accepted: 09/14/2024] [Indexed: 11/28/2024]
Abstract
Although sediment dredging is a widely employed water management and restoration technique for the removal of internal nitrogen (N), the long-term effects of dredging on N transformation in dredged rivers remain largely undetermined. In this study, we investigated the effects of dredging on N transformation processes spanning three years at ten sites in the purple-soil watershed within the middle reaches of the Fu River Basin. We combined isotopic and molecular techniques to provide novel insights into the interactions associated with microbial utilization capacities between sediment and river water before, during, and after dredging. Initially, dredging was found to significantly reduce the total nitrogen content by approximately 75 %, although over time, there was a slight increase in concentrations. Secondly, significant reductions in microbial richness and diversity were detected in both river water and sediment, with 39 classes reduced, 12 new classes emerging, and an increase in archaea, reshaping the microbial community. Lastly, dredging was found to promote a significant shift in functional contributions, with increases in the abundance of key enzyme activities (1.7.5.1 and 1.7.2.5) and denitrification genes (nirK, norB, and nosZ). This enhancement notably promoted denitrification and dissimilatory nitrate reduction to ammonium (DNRA), accompanied by significant environmental changes in sediment and river water. These changes facilitated the removal of nitrates in the Xiangshuitan watershed. Our study overcomes the limitations associated with watershed and microenvironment scales, providing insights into the mechanisms where by dredging activities influence the interplay between external and internal N transformations.
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Affiliation(s)
- Zhuo Hao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Shibo Chen
- Development Research Center of the Ministry of Water Resources of PR China, Beijing, 100038, China
| | - Qingwen Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bing Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Lai KP, Boncan DAT, Qin X, Chan TF, Tse WKF. Roles and occurrences of microbiota in the osmoregulatory organs, gills and gut, in marine medaka upon hypotonic stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101285. [PMID: 39002350 DOI: 10.1016/j.cbd.2024.101285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/15/2024]
Abstract
Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na+/K+-atpase, and cftr, were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress.
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Affiliation(s)
- Keng Po Lai
- Key Laboratory of Environmental Pollution and Integrative Omics, Education Department of Guangxi Zhuang Autonomous Region, Guilin Medical University, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China.
| | - Delbert Almerick T Boncan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xian Qin
- Department of Chemistry, City University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
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Sharma N, Das BK, Bhattacharjya BK, Chaudhari A, Behera BK, Kumar AP, Chakraborty HJ. Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India. Front Microbiol 2024; 15:1426463. [PMID: 39633804 PMCID: PMC11614985 DOI: 10.3389/fmicb.2024.1426463] [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: 05/01/2024] [Accepted: 10/29/2024] [Indexed: 12/07/2024] Open
Abstract
Introduction The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments. Methods The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment. Results and discussion Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, β-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.
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Affiliation(s)
- Niti Sharma
- ICAR-Central Inland Fisheries Research Institute, Regional Centre, Guwahati, Assam, India
| | | | | | - Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | | | - Annam Pavan Kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
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Martinez O, Bergen SR, Gareis JB. Comparison of Yamuna (India) and Mississippi River (United States of America) bacterial communities reveals greater diversity below the Yamunotri Glacier. PLoS One 2024; 19:e0304664. [PMID: 38968225 PMCID: PMC11226128 DOI: 10.1371/journal.pone.0304664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/15/2024] [Indexed: 07/07/2024] Open
Abstract
The Yamuna River in India and the Mississippi River in the United States hold significant commercial, cultural, and ecological importance. This preliminary survey compares the bacterial communities sampled in surface waters at 11 sites (Yamuna headwaters, Mississippi headwaters, Yamuna River Yamunotri Town, Mississippi River at Winona, Tons River, Yamuna River at Paonta Sahib, Yamuna River Delhi-1, Yamuna River Delhi-2, Yamuna River before Sangam, Sangam, Ganga River before Sangam). Bacterial 16S rDNA analyses demonstrate dominance of Proteobacteria and Bacteroidetes phyla. Actinobacteria were also dominant at sites near Sangam in India and sites in Minnesota. A dominance of Epsilonbacteraeota were found in Delhi, India. Principal component analysis (PCA) using unique operational taxonomic units (OTUs) resulted in the identification of 3 groups that included the Yamuna River locations in Delhi (Delhi locations), Yamuna headwaters and Yamuna River at Yamunotri (Yamuna River locations below the Glacier) and Mississippi, Ganga, Tons, and other Yamuna River locations. Diversity indices were significantly higher at the Yamuna River locations below the Glacier (Simpson D = 0.986 and Shannon H = 5.06) as compared (p value <0.001) to the Delhi locations (D = 0.951 and H = 4.23) and as compared (p value < 0.001) to Mississippi, Ganga, Tons, and other Yamuna River locations (D = 0.943 and H = 3.96). To our knowledge, this is the first survey to compare Mississippi and Yamuna River bacterial communities. We demonstrate higher diversity in the bacterial communities below the Yamunotri glacier in India.
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Affiliation(s)
- Osvaldo Martinez
- Biology Department, Winona State University, Winona, MN, United States of America
| | - Silas R. Bergen
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
| | - Jacob B. Gareis
- Mathematics and Statistics Department, Winona State University, Winona, MN, United States of America
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Rout AK, Dixit S, Tripathy PS, Rout SS, Parida SN, Parida PK, Sarkar DJ, Kumar Das B, Singh AK, Behera BK. Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134377. [PMID: 38663298 DOI: 10.1016/j.jhazmat.2024.134377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024]
Abstract
The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar 751003, India
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Sushree Swati Rout
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Satya Narayan Parida
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Ashok Kumar Singh
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India.
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Liu S, Pan Y, Jin X, Zhao S, Xu X, Chen Y, Shen Z, Chen C. A novel Biochar-PGPB strategy for simultaneous soil remediation and safe vegetable production. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124254. [PMID: 38815893 DOI: 10.1016/j.envpol.2024.124254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/08/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
There is currently increasing pressure on agriculture to simultaneously remediate soil and ensure safe agricultural production. In this study, we investigate the potential of a novel combination of biochar and plant growth-promoting bacteria (PGPB) as a promising approach. Two types of biochar, corn stover and rice husk-derived, were used in combination with a PGPB strain, Bacillus sp. PGP5, to remediate Cd and Pb co-contaminated soil and enhance lettuce performance. The contaminated soil was pre-incubated with biochar prior to PGP5 inoculation. The combined application of biochar and PGPB reduced the diethylenetriaminepentaacetic acid (DTPA) -extractable Cd and Pb concentrations in the soil by 46.45%-55.96% and 42.08%-44.83%, respectively. Additionally, this combined application increased lettuce yield by 23.37%-65.39% and decreased Cd and Pb concentrations in the edible parts of the lettuce by 57.39%-68.04% and 13.57%-32.50%. The combined application showed a better promotion on lettuce growth by facilitating chlorophyll synthesis and reducing oxidative stress. These demonstrated a synergistic effect between biochar and PGPB. Furthermore, our study elucidated the specific role of the biochar-PGPB combination in soil microbial communities. Biochar application promoted the survival of PGP5 in the soil. The impact of biochar or PGPB on microbial communities was found to be most significant in the early stage, while the development of plants had a greater influence on rhizosphere microbial communities in later stage. Plants showed a tendency to recruit plant-associated microbes, such as Cyanobacteria, to facilitate growth processes. Notably, the combined application of biochar and PGPB expedited the assembly of microbial communities, enabling them more closely with the rhizosphere microbial communities in late stage of plant development and thus enhancing their effects on promoting plant growth. This study highlights the "accelerating" advantage of the biochar-PGPB combination in the assembly of rhizosphere microbiomes and offers a new strategy for simultaneous soil remediation and safe agricultural production.
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Affiliation(s)
- Sijia Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yiwen Pan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, Zhejiang, China
| | - Shangjun Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiaohong Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China; Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Ye Y, Peng C, Zhu D, Yang R, Deng L, Wang T, Tang Y, Lu L. Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169299. [PMID: 38104834 DOI: 10.1016/j.scitotenv.2023.169299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/20/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.
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Affiliation(s)
- Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637009, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Ruiyu Yang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Linjie Deng
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Tao Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Nanchong City of Ecological Environment Protection and Pollution Prevention in Jialing River Basin, China West Normal University, Nanchong 637009, China.
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Li Y, Lou D, Zhou X, Zhuang X, Wang C. Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge. PeerJ 2024; 12:e16931. [PMID: 38371377 PMCID: PMC10874175 DOI: 10.7717/peerj.16931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Background Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability. Methods In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis. Results The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments.
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Affiliation(s)
- Yishi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- Focused Photonics (Hangzhou), Inc., Hangzhou, Zhejiang, China
| | - Daoming Lou
- Hangzhou Urban Water Facilities and River Conservation Management Center, Hangzhou, Zhejiang, China
| | - Xiaofei Zhou
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | - Xuchao Zhuang
- Focused Photonics (Hangzhou), Inc., Hangzhou, Zhejiang, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
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Wang JX, Li P, Chen CZ, Liu L, Li ZH. Biodegradation of sulfadiazine by ryegrass (Lolium perenne L.) in a soil system: Analysis of detoxification mechanisms, transcriptome, and bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132811. [PMID: 37866149 DOI: 10.1016/j.jhazmat.2023.132811] [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: 07/26/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
The indiscriminate use of sulfadiazine has caused severe harm to the environment, and biodegradation is a viable method for the removal of sulfadiazine. However, there are few studies that consider sulfadiazine biodegradation mechanisms. To comprehensively investigate the process of sulfadiazine biodegradation by plants in a soil system, a potted system that included ryegrass and soil was constructed in this study. The removal of sulfadiazine from the system was found to be greater than 95% by determining the sulfadiazine residue. During the sulfadiazine removal process, a significant decrease in ryegrass growth and a significant increase in antioxidant enzyme activity were observed, which indicates the toxic response and detoxification mechanism of sulfadiazine on ryegrass. The ryegrass transcriptome and soil bacterial communities were further investigated. These results revealed that most of the differentially expressed genes (DEGs) were enriched in the CYP450 enzyme family and phenylpropanoid biosynthesis pathway after sulfadiazine exposure. The expression of these genes was significantly upregulated. Sulfadiazine significantly increased the abundance of Vicinamibacteraceae, RB41, Ramlibacter, and Microvirga in the soil. These key genes and bacteria play an important role in sulfadiazine biodegradation. Through network analysis of the relationship between the DEGs and soil bacteria, it was found that many soil bacteria promote the expression of plant metabolic genes. This mutual promotion enhanced the sulfadiazine biodegradation in the soil system. This study demonstrated that this pot system could substantially remove sulfadiazine and elucidated the biodegradation mechanism through changes in plants and soil bacteria.
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Affiliation(s)
- Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
| | | | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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Rout AK, Tripathy PS, Dixit S, Behera DU, Behera B, Das BK, Behera BK. Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India. Antibiotics (Basel) 2023; 12:1735. [PMID: 38136769 PMCID: PMC10740832 DOI: 10.3390/antibiotics12121735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway;
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Dibyajyoti Uttameswar Behera
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
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Srivastava A, Verma D. Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India. World J Microbiol Biotechnol 2023; 39:294. [PMID: 37656255 DOI: 10.1007/s11274-023-03730-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
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Srivastava A, Verma D. Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27552-7. [PMID: 37217817 DOI: 10.1007/s11356-023-27552-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
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