Depth-resolved transcriptional activity of antibiotic resistance genes in deep permafrost of the Qinghai–Tibet Plateau

The Qinghai-Tibet Plateau harbors permafrost ecosystems containing diverse antibiotic resistance genes (ARGs), yet their transcriptional activity and depth-resolved patterns remain poorly understood. Here, we performed meta-transcriptomic profiling of two permafrost cores (40-m and 100-m) from the Tuotuo River Basin. Within each core, permafrost layers exhibited higher relative ARG transcript abundance and diversity than overlying active layers. β-Lactam, multidrug, and puromycin resistance transcripts were enriched in permafrost, whereas aminoglycoside resistance predominated in the active layer. Antibiotic inactivation mechanisms were more prevalent in permafrost, while target modification dominated in the active layer within the analyzed cores. Plasmid-associated ARGs were detected, and mobile genetic elements (MGEs) showed stratified distributions, with integrative and conjugative elements more abundant in active layers and integrons enriched in permafrost strata. ARG transcript levels were associated with microbial community composition, MGEs, metal tolerance genes, and trace metal concentrations. Neutral community modeling suggested that ARG assemblages are largely consistent with stochastic processes, indicating long-term persistence under environmental filtering. As the analysis is limited to two cores, these observations reflect site-specific transcriptional patterns rather than generalizable regional trends. Overall, this study provides evidence of ARG transcripts in permafrost layers, offering a baseline for future investigations of resistome dynamics under thaw conditions.