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.