Elevated CO₂ Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO₂ Enrichment (FACE) Experiment

Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO₂ on seed resistomes remains poorly understood. Here, a free-air CO₂ enrichment system was used to examine the impact of elevated CO₂ on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO₂ levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO₂ levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO₂ level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO₂ directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO₂ on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.