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<p>The Varuna River, a polluted tributary of the Ganges in Varanasi, India, receives extensive anthropogenic inputs from urban, industrial, and agricultural sources. To characterize microbial community structure and antimicrobial resistance (AMR) gene distribution along a spatial gradient, we performed whole-genome shotgun metagenomic sequencing of water samples from four sites spanning upstream reference (VRG) to downstream Ganga confluence (VAG). Taxonomic profiling using GTDB-Tk revealed progressive diversity loss downstream (Shannon index: VRG 6.74 to VAG 6.24) with shifts from aerobic freshwater taxa (<i>Hydrogenophaga</i>,<i> Rhizobium</i>) to anaerobic pollution-tolerant genera (<i>Desulfobacter</i>, <i>Acidovorax</i>). Downstream sites exhibited elevated abundances of taxa that include potential pathogens (<i>Escherichia coli</i>, <i>Pseudomonas aeruginosa</i>, <i>Acinetobacter baumannii</i>). AMR gene analysis using AMRFinderPlus demonstrated dramatic accumulation from upstream to downstream: 5 to 51 genes (92% increase) extending from 4 to 13 resistance classes. Critical resistance genes detected include carbapenemases (<i>blaCAU</i>), extended-spectrum beta-lactamases (<i>blaGES-1</i>, <i>blaVEB-9</i>), quinolone resistance (<i>qnrVC1</i>), and fosfomycin resistance (<i>fosA</i>). The downstream confluence site (VAG) represents a maximum AMR reservoir with resistance to WHO-critical antibiotics. AMR gene profiles also varied across all 4 sampling sites. Thus, this study provides the first metagenomic baseline for Varuna River microbial communities and resistomes, identifying spatial patterns along the upstream-downstream gradient consistent with potential urbanization influence on the ecosystem structure indicate that VAG as a priority site for water quality surveillance and future environmental study. Limitations of the present study includes the single composite samples per site and absence of environmental chemistry data that could be the basis for future integrative studies.</p> Graphical Abstract <p></p>

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Environmental Impact of Bacterial Communities and Anti-Microbial Resistance Genes in the River Varuna: A Metagenomic Approach

  • 期刊论文

  • 发表日期：

    2026年6月22日

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  • Arpit Srivastava,
  • Piyush Kant Rai,
  • Shreyansh Parsai,
  • Kamlesh Choure,
  • Reena Vishvakarma

摘要

The Varuna River, a polluted tributary of the Ganges in Varanasi, India, receives extensive anthropogenic inputs from urban, industrial, and agricultural sources. To characterize microbial community structure and antimicrobial resistance (AMR) gene distribution along a spatial gradient, we performed whole-genome shotgun metagenomic sequencing of water samples from four sites spanning upstream reference (VRG) to downstream Ganga confluence (VAG). Taxonomic profiling using GTDB-Tk revealed progressive diversity loss downstream (Shannon index: VRG 6.74 to VAG 6.24) with shifts from aerobic freshwater taxa (Hydrogenophaga, Rhizobium) to anaerobic pollution-tolerant genera (Desulfobacter, Acidovorax). Downstream sites exhibited elevated abundances of taxa that include potential pathogens (Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii). AMR gene analysis using AMRFinderPlus demonstrated dramatic accumulation from upstream to downstream: 5 to 51 genes (92% increase) extending from 4 to 13 resistance classes. Critical resistance genes detected include carbapenemases (blaCAU), extended-spectrum beta-lactamases (blaGES-1, blaVEB-9), quinolone resistance (qnrVC1), and fosfomycin resistance (fosA). The downstream confluence site (VAG) represents a maximum AMR reservoir with resistance to WHO-critical antibiotics. AMR gene profiles also varied across all 4 sampling sites. Thus, this study provides the first metagenomic baseline for Varuna River microbial communities and resistomes, identifying spatial patterns along the upstream-downstream gradient consistent with potential urbanization influence on the ecosystem structure indicate that VAG as a priority site for water quality surveillance and future environmental study. Limitations of the present study includes the single composite samples per site and absence of environmental chemistry data that could be the basis for future integrative studies.

Graphical Abstract