Background The Yamuna River, one of India’s major freshwater systems, has experienced severe ecological deterioration due to the continuous discharge of untreated domestic and industrial effluents, resulting in high microbial and chemical pollution loads. This degradation has promoted the proliferation of pathogenic and antimicrobial-resistant bacteria, underscoring the urgent need for sustainable microbial control strategies. Methods This study comprehensively characterized the bacteriophage diversity of the Yamuna River through an integrative approach combining conventional phage isolation, transmission electron microscopy (TEM), and high-throughput metagenomic analysis. Results Phages infecting Escherichia coli and Pseudomonas fluorescens exhibited distinct plaque morphologies and strong lytic activity, confirming the presence of active viral populations. TEM analysis revealed diverse tailed morphotypes characteristic of the class Caudoviricetes. Metagenomic profiling identified 28,993 viral contigs across 21 viral classes, predominantly Caudoviricetes (49%). Of these, 57% were classified phages, while 43% remained unclassified, indicating substantial unexplored viral diversity within this ecosystem. Notably, 19% of the detected phages were associated with pathogenic bacterial hosts, including multidrug-resistant (MDR) ESKAPE pathogens of 544 abundance (4%), highlighting their clinical and ecological significance. Functional annotation further revealed auxiliary metabolic genes (AMGs) involved in nutrient cycling, host metabolism modulation, and viral replication, reflecting the adaptive versatility of these phages. Conclusion This study presents an integrated, phage-centric investigation from the polluted water column of the Yamuna River in Delhi. By combining wet-lab isolation, transmission electron microscopy, and metagenomic analysis of bacteriophages, we identify a diverse reservoir of largely uncultivated waterborne phages with relevance to microbial regulation, environmental monitoring, and antimicrobial resistance mitigation. These findings provide a genomic basis for exploring environmental phages in sustainable water quality management and the development of phage-based therapeutic interventions. Graphical Abstract

Metagenome-based insights into bacteriophage diversity of an urban river ecosystem

期刊论文
发表日期：

2026年3月31日

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Abhiruchi Varshney,
Indira P. Sarethy

摘要

Background

The Yamuna River, one of India’s major freshwater systems, has experienced severe ecological deterioration due to the continuous discharge of untreated domestic and industrial effluents, resulting in high microbial and chemical pollution loads. This degradation has promoted the proliferation of pathogenic and antimicrobial-resistant bacteria, underscoring the urgent need for sustainable microbial control strategies.

Methods

This study comprehensively characterized the bacteriophage diversity of the Yamuna River through an integrative approach combining conventional phage isolation, transmission electron microscopy (TEM), and high-throughput metagenomic analysis.

Results

Phages infecting Escherichia coli and Pseudomonas fluorescens exhibited distinct plaque morphologies and strong lytic activity, confirming the presence of active viral populations. TEM analysis revealed diverse tailed morphotypes characteristic of the class Caudoviricetes. Metagenomic profiling identified 28,993 viral contigs across 21 viral classes, predominantly Caudoviricetes (49%). Of these, 57% were classified phages, while 43% remained unclassified, indicating substantial unexplored viral diversity within this ecosystem. Notably, 19% of the detected phages were associated with pathogenic bacterial hosts, including multidrug-resistant (MDR) ESKAPE pathogens of 544 abundance (4%), highlighting their clinical and ecological significance. Functional annotation further revealed auxiliary metabolic genes (AMGs) involved in nutrient cycling, host metabolism modulation, and viral replication, reflecting the adaptive versatility of these phages.

Conclusion

This study presents an integrated, phage-centric investigation from the polluted water column of the Yamuna River in Delhi. By combining wet-lab isolation, transmission electron microscopy, and metagenomic analysis of bacteriophages, we identify a diverse reservoir of largely uncultivated waterborne phages with relevance to microbial regulation, environmental monitoring, and antimicrobial resistance mitigation. These findings provide a genomic basis for exploring environmental phages in sustainable water quality management and the development of phage-based therapeutic interventions.

Graphical Abstract