Influence of Urban Wastewater and Pig Farming on Aquatic Microbiomes and Waterborne Pathogens in Southern Brazil

Abstract Urbanization and intensive animal farming generate large volumes of waste that introduce microbial contaminants into aquatic ecosystems, increasing the risk of pathogen dissemination. We analyzed 16S rRNA-based microbial community profiles from water samples collected upstream and downstream of pig farms and urban areas in southern Brazil including Itambaracá (P1, P3), Chapecó (P2, P4), Curitiba (P5) and Joinville (P6). Proteobacteria dominated most samples, with Gammaproteobacteria enriched near pig farming sites. Urban-impacted waters showed reduced microbial diversity and clear taxonomic shifts consistent with wastewater influence. Notably, pathogenic bacteria of public health concern, including Escherichia coli O157:H7, Shigella flexneri 2a, and Pseudomonas aeruginosa, were detected in areas affected by livestock production and urban effluent discharge. These findings demonstrate that animal production systems and urban wastewater may act as interconnected sources of environmental contamination, reshaping aquatic microbiomes and introducing clinically relevant pathogens into natural waters. This convergence highlights the need for integrated monitoring and management strategies to protect ecosystem integrity and reduce human health risks.