From Source to Estuary: Spatiotemporal Dynamics of Water Quality, Microbial Communities, Antimicrobial Resistance, and Bacteriophage Diversity in the Ganga River

Abstract

The Ganga River is one of the world's most important freshwater ecosystems, sustaining millions of people while increasingly experiencing anthropogenic stress from urbanization, industrial discharge, agricultural runoff, and untreated sewage. This study investigated spatial and seasonal variations in water quality, microbial diversity, antimicrobial resistance, metal tolerance, and bacteriophage distribution along the river. Water samples were collected from 17 sites spanning the upper, middle, and lower Ganga during summer, monsoon, and winter, yielding 51 sampling events. Physicochemical parameters, coliform abundance, culture-based bacterial identification, antibiotic and metal tolerance assays, bacteriophage isolation, and phage-marker PCR screening were performed. Upstream sites exhibited comparatively low turbidity, TSS, BOD, COD, and microbial loads, whereas middle and downstream stretches showed significantly elevated values, particularly during the monsoon season. Coliform counts frequently exceeded 1000 MPN/100 mL, indicating substantial faecal contamination. The predominant culturable bacteria included Escherichia coli and Pseudomonas aeruginosa, together with other environmental and enteric taxa. These isolates displayed variable tolerance to tetracycline, levofloxacin, azithromycin, and selected metals, reflecting potential adaptation to persistent environmental stressors. Diverse bacteriophage populations and phage-associated genetic markers were detected across river stretches, indicating active phage–host interactions. Overall, the findings demonstrate that anthropogenic inputs and seasonal hydrological changes strongly influence microbial ecology and resistance patterns in the Ganga River, highlighting the need for continuous monitoring and improved wastewater management to safeguard ecosystem and public health.