Evaluation of the Abundance of Microplastics and Antibiotic Resistance Genes in the Upper Ganga Canal during the Yearly Desilting Cycle

The current study focuses on the impact of annual desilting of the Upper Ganga Canal (UGC) on the dynamics of antibiotic resistance genes (ARGs) and microplastics (MPs), based on land use. Although the annual desilting of the UGC is conducted to maintain hydraulic flow, the ecological impacts of this activity on emerging contaminants remain poorly understood. Grab surface water samples were collected before and after desilting of the UGC (November–December 2024) and analyzed for three genetic markers (including 16S rRNA, yccT, and intI1) and five ARGs (blaTEM, tetA, ermF, czcA, and qnrS) using qPCR; two antimicrobials (ciprofloxacin and triclosan) using LC–MS/MS; MPs using micro-Raman spectroscopy; and total suspended solids (TSS) and dissolved oxygen (DO). The DO showed no significant change across sites post-desilting, whereas TSS increased consistently, indicating sediment disturbance and particulate resuspension. MPs were dominated by polyethylene (PE), polystyrene (PS), and polyvinyl chloride (PVC) at all sites. The levels of 16S rRNA gene copies increased at all sampling locations after desilting, except at site S2 (Jwalapur; urban residential, low intensity), where 16S rRNA gene copies decreased. A six-log decrease in the relative abundance of tetA was observed at site S2 after desilting, representing the largest change recorded in the study. The concentrations of ciprofloxacin and triclosan increased at site S3 after desilting; similar results were observed at site S4 (Dhanuri Village; agricultural, high intensity) and site S5 (Piran Kaliyar; residential, high intensity). Multivariate and correlation analyses indicated that desilting altered interaction networks among ARGs, MPs, and antibiotics. Post-desilting, a very strong correlation emerged between intI1 and blaTEM (ρ = 0.94), whereas triclosan correlated positively with qnrS (ρ = 0.77) and with ciprofloxacin (ρ = 0.60), consistent with co-selection dynamics. Shifts were also observed in size class and polymer-specific associations (e.g., PE with ciprofloxacin and triclosan), suggesting transient mobilization and adsorption processes following sediment disturbance. Overall, although annual desilting reduced certain ARGs locally (e.g., tetA at S2), it coincided with increases in other ARGs and co-selectors and strengthened select ARG–antimicrobial linkages, implying short-term antimicrobial resistance (AMR) risk trade-offs. These results support optimizing both the frequency and methodology of UGC desilting to retain hydraulic benefits while mitigating unintended AMR impacts.