Persistent soil resistome expansion following bacterial inoculation despite successful antibiotic bioremediation

While antibiotic-degrading bacteria (ADB) are anticipated as sustainable tools to mitigate environmental pollution, current assessments often prioritize degradation efficiency over the ecological risks posed by their genetic materials. Using a tetracycline antibiotics-degrading bacterium Glutamicibacter nicotianae OTC-16 in microcosms with two contrasting soils, we found that strain OTC-16 accelerated oxytetracycline dissipation but also triggered persistent expansion of the soil resistome under the tested conditions. This expansion was driven mainly by co-carried passenger antibiotic resistance genes (ARGs) rather than tetracycline ARGs. The fates of inoculant-carried ARGs diverged markedly. While the functional gene tet(33) was rapidly purged after selective pressure was removed, passenger ARGs such as sul1 and qacEΔ1 persisted much longer. Soil background strongly shaped these patterns. In the soil with a relatively simple background resistome, strain OTC-16 established more successfully and left a stronger inoculant-derived resistome expansion. In the soil with a more complex background resistome, long-term colonization was not sustained, although passenger ARGs persisted as relic DNA and part of the resistome expansion involved the indigenous non-tetracycline resistome. Genomic survey of 26 publicly available tetracycline-degrading bacterial genomes further suggested that plasmid-borne passenger ARGs are common among known ADB, indicating that the risk observed here may not be unique to strain OTC-16. These findings show that successful antibiotic bioremediation does not necessarily reduce resistome risk, and that future evaluation and design of ADB should consider not only remediation efficiency, but also passenger ARG burden and long-term genetic aftereffects.