Background: The leaching of toxicants from informal electronic waste (e-waste) processing sites into urban aquifers is a pressing environmental and public health concern. While the geochemical impacts are documented, the consequences for subsurface microbial ecosystems—critical for groundwater biogeochemistry and natural attenuation—remain poorly understood.
Objective: This study aimed to characterize the structural and functional shifts in microbial communities within urban groundwater influenced by e-waste leachate, linking these changes to heavy metal and organic contaminant profiles.

Methods: Groundwater samples were collected from 16 monitoring wells along a defined contamination gradient (0 to 450 meters) from a major informal e-waste dismantling zone. Samples underwent inductively coupled plasma mass spectrometry (ICP-MS) for heavy metals, gas chromatography-mass spectrometry (GC-MS) for organic contaminants (PBDEs, PCBs), and high-throughput 16S rRNA gene sequencing (Illumina MiSeq platform). Functional potential was inferred via PICRUSt2 analysis. Multivariate statistical analysis (RDA, PERMANOVA) was performed to correlate microbial data with geochemistry.
Results: Concentrations of lead (Pb: 12.5–1450 µg/L), cadmium (Cd: 0.8–42.3 µg/L), and polybrominated diphenyl ethers (PBDEs: 5–310 ng/L) exceeded WHO and EPA guidelines in proximal wells. Microbial alpha diversity (Shannon index) decreased significantly (p < 0.001) with proximity to the contamination source. Community structure was profoundly altered (PERMANOVA, R² = 0.62, p = 0.001), with a decline in putative groundwater beneficial taxa like Gallionellaceae and Nitrospira. Conversely, a significant enrichment (p< 0.01) of metal-resistant (e.g., Geobacter, Thiobacillus) and organic-degrading genera (e.g., Sphingomonas, Pseudomonas) was observed. Functional prediction indicated an increase in genes related to heavy metal efflux (czcA, copA) and horizontal gene transfer.

Conclusion: E-waste leachate induces severe toxic pressure, leading to a loss of microbial diversity and a selection for specialized, resistant consortia. This shift potentially compromises essential biogeochemical services (e.g., denitrification) while promoting pathways for contaminant co-tolerance and gene mobilization. The findings underscore the need to integrate microbial ecosystem health into risk assessments of e-waste contaminated aquifers.