Metagenomic Insights Delineating the Impact of Copper Oxide Nanoparticles on Microbial Community Structure of Yamuna River Water

The Yamuna River is one of the most polluted freshwater bodies in India. High levels of microbial and chemical contaminants pose serious environmental and public health concerns. The present study evaluated the potential of mycogenic copper oxide nanoparticles (CuO NPs) for the remediation of contaminated Yamuna River water and their influence on microbial community structure using metagenomic analysis. CuO NPs were synthesized using Serendipita indica and characterized using multiple analytical techniques. The water samples were collected from the Wazirabad stretch of Yamuna river, one of the most heavily polluted section of Delhi. The samples were treated at different concentrations of CuO NPs ranging between 25–125 ppm. Physicochemical parameters including pH, total dissolved solids (TDS), total suspended solids (TSS), biological oxygen demand (BOD), chemical oxygen demand (COD), turbidity, nutrients, and heavy metal content were measured before and after treatment. Changes in prokaryotic and eukaryotic community composition were assessed through high-throughput metagenomic sequencing. Among the tested concentrations, 100 ppm CuO NPs showed the best remediation performance. The highest removal efficiency were observed for turbidity (81.82%), nitrate (82.18%), sulphate (77.78%) and TDS (78.00%). Significant improvements were also recorded in other water quality parameters. Metagenomic analysis indicated substantial shifts in microbial community structure following treatment. The relative abundance of several pollution-associated and potentially pathogenic taxa decreased markedly. These included members of Pseudomonadota, Oomycota , Thauera , Acidovorax , and Hyaloperonospora . The treatment also reduced the abundance of fungal and protozoan contaminants. The observed microbial changes were likely driven by multiple factors. Reduction in nutrient and organic pollutant concentrations limited the growth of pollution-adapted microorganisms. In addition, the intrinsic antimicrobial activity of CuO NPs contributed to microbial suppression through reactive oxygen species (ROS) generation and disruption of cellular membranes. Overall, the findings demonstrate that mycogenic CuO NPs are effective in improving water quality and reshaping microbial communities in contaminated river water. This green nanotechnology approach offers a promising strategy for the development of sustainable and next-generation wastewater and river-water remediation systems.