The discharge of untreated waste serves as a major source of environmental pollution, impacting both terrestrial and aquatic ecosystems. Although the microbial diversity within these environments is remarkably high, scientific investigation into their ecological functions, metabolic capabilities, and pathogenic risks remains limited.

In this study, we employed Illumina sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene to characterize microbial diversity and functional attributes across four distinct polluted sites involving soil (Site 1) and river (Sites 2–4). Across all locations, Proteobacteria and Bacteroidetes emerged as the dominant microbial phyla; however, the presence and abundance of specific phyla varied distinctly across sites. In the present study, dentification of several potential pathogens was detected. Functional annotation analyses revealed that genes associated with amino acid and carbohydrate metabolism were highly abundant at these sites. Furthermore, genes conferring antibiotic resistance and xenobiotic degradation were also observed.

These findings indicate that polluted ecosystems are metabolically active and serve as reservoirs for potential pathogenic microorganisms; consequently, they pose significant risks to both the environment and public health. This study provides critical insights into the dynamics of microbial communities in waste-contaminated environments and underscores the imperative of adopting integrated management strategies to curb the proliferation of pathogenic microorganisms.