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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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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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Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li DD, Tu Q. Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front Microbiol 2023; 14:1291242. [PMID: 38053549 PMCID: PMC10694361 DOI: 10.3389/fmicb.2023.1291242] [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: 09/08/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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Liu H, Zhang H, Yu Q, Zhang S, Tu X, Zhuang F, Fu S. Lead induced structural and functional damage and microbiota dysbiosis in the intestine of crucian carp ( Carassius auratus). Front Microbiol 2023; 14:1239323. [PMID: 37731918 PMCID: PMC10507410 DOI: 10.3389/fmicb.2023.1239323] [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: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Lead (Pb) is a hazardous pollutant in water environments that can cause significant damage to aquatic animals and humans. In this study, crucian carp (Carassius auratus) were exposed to waterborne Pb for 96 h; then, histopathological analysis, quantitative qPCR analysis, and 16S high-throughput sequencing were performed to explore the effects of Pb on intestinal bioaccumulation, structural damage, oxidative stress, immune response, and microbiota imbalance of C. auratus. After Pb exposure, the intestinal morphology was obviously damaged, including significantly increasing the thickness of the intestinal wall and the number of goblet cells and reducing the depth of intestinal crypts. Pb exposure reduced the mRNA expressions of Claudin-7 and villin-1 while significantly elevated the level of GST, GSH, CAT, IL-8, IL-10, IL-1, and TNF-α. Furthermore, 16S rRNA analysis showed that the Shannon and Simpson indices decreased at 48 h after Pb exposure, and the abundance of pathogenic bacteria (Erysipelotrichaceae, Weeksellaceae, and Vibrionaceae) increased after Pb exposure. In addition, the correlation network analysis found that Proteobacteria were negatively correlated with Firmicutes and positively correlated with Bacteroidetes. Functional prediction analysis of bacteria speculated that the change in intestinal microbiota led to the PPAR signaling pathway and peroxisome function of the intestine of crucian carp was increased, while the immune system and membrane transport function were decreased. Finally, canonical correlation analysis (CCA) found that there were correlations between the intestinal microbiota, morphology, antioxidant factors, and immune factors of crucian carp after Pb exposure. Taken together, our results demonstrated that intestinal flora dysbiosis, morphological disruption, oxidative stress, and immune injury are involved in the toxic damage of Pb exposure to the intestinal structure and function of crucian carp. Meanwhile, Pb exposure rapidly increased the abundance of pathogenic bacteria, leading to intestinal disorders, further aggravating the damage of Pb to intestinal structure and function. These findings provide us a basis for the link between gut microbiome changes and heavy metal toxicity, and gut microbiota can be used as biomarkers for the evaluation of heavy metal pollution in future.
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Affiliation(s)
- Haisu Liu
- Research Center of Harmful Algae and Marine Biology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hang Zhang
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Information Center, Wuhan, China
| | - Qianxun Yu
- Hubei Institute of Product Quality Supervision and Inspection, Wuhan, China
| | - Sanshan Zhang
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiao Tu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Fenghong Zhuang
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shengli Fu
- School of Life Sciences, South China Normal University, Guangzhou, China
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Morshed SM, Chen YY, Lin CH, Chen YP, Lee TH. Freshwater transfer affected intestinal microbiota with correlation to cytokine gene expression in Asian sea bass. Front Microbiol 2023; 14:1097954. [PMID: 37089546 PMCID: PMC10117908 DOI: 10.3389/fmicb.2023.1097954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
As a catadromous fish, Asian sea bass (Lates calcarifer) juveniles migrate from seawater (SW) to freshwater (FW) for growth and development. During migration, they undergo physiological changes to acclimate to environmental salinity. Thus, it is crucial to understand how SW-to-FW migration affects the gut microbiota of catadromous fish. To the best of our knowledge, no study has revealed the effects of transfer to hypotonic environments on a catadromous fish microbiota. In this study, we aimed to determine the effects of FW transfer on the microbiota and cytokine gene expression in the intestines of juvenile catadromous Asian sea bass. The relationship between the water and the gut microbiota of this euryhaline species was also examined. We found that FW transfer affected both mucosa- and digesta-associated microbiota of Asian sea bass. Plesiomonas and Cetobacterium were dominant in both the mucosa- and digesta-associated microbiota of FW-acclimated sea bass. The pathogenic genera Vibrio, Staphylococcus, and Acinetobacter were dominant in the SW group. Although dominant fish microbes were present in the water, fish had their own unique microbes. Vitamin B6 metabolism was highly expressed in the FW fish microbiota, whereas arginine, proline, and lipid metabolism were highly expressed in the SW fish microbiota. Additionally, the correlation between cytokine gene expression and microbiota was found to be affected by FW transfer. Taken together, our results demonstrated that FW transfer altered the composition and functions of mucosa- and digesta-associated microbiota of catadromous Asian sea bass intestines, which correlated with cytokine gene expression.
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Affiliation(s)
- Syed Monzur Morshed
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Yi Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Hao Lin
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Yen-Po Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Yen-Po Chen,
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Tsung-Han Lee,
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