Metabolic retraction and virulence expansion in a tropical urban river microbiome under dry-season stress

Anowara Begum , Muhammad Ehteshamul Haque, Md. Shaminur Rahman, Munawar Sultana 

Anthropogenic pollution and seasonal flow reduction concentrate untreated organic waste in tropical rivers, yet the coupled response of microbial metabolism and virulence gene repertoires remains poorly understood. We applied shotgun metagenomics to the Shitalakshya River (Bangladesh) from early (December 2024) to peak (February 2025) dry season. Dissolved oxygen fell to near-hypoxic levels, ammonia nearly doubled (5.1 → 9.95 mg L⁻¹), and total organic carbon surged. KEGG profiling revealed a contracting metabolic core, with amino acid, carbohydrate, and energy metabolism declining by 59–86%, while xenobiotic biodegradation rose 4.6-fold and secondary metabolite biosynthesis 7.4-fold. Network analysis segregated the microbiome into a shrinking growth-associated module and an expanding detoxification cluster. Parallel virulence gene profiling (VFDB) uncovered a 39% increase in total abundance and a 29% richer gene repertoire. Motility and chemotaxis genes nearly doubled, biofilm determinants (algD, alg8, mrk operon) emerged de novo, and Type VI secretion system components became markedly enriched. Conversely, siderophore-mediated iron acquisition and immune evasion factors declined substantially. These coordinated shifts indicate a transition from growth-oriented metabolism to persistence strategies based on environmental sensing and surface colonization. The co-enrichment of motility, biofilm, and T6SS traits alongside pollution-responsive pathways highlights a dual ecological filter wherein dry-season stress simultaneously selects for xenobiotic-tolerant generalists and opportunistic pathogens. Our findings establish a quantitative framework linking seasonal pollution to enhanced pathogenicity potential in urban rivers, with direct implications for drinking water abstraction and public health monitoring.