Antibiotic-degrading bacteria shape resistome dynamics and horizontal gene transfer potential in soils with contrasting properties

TL;DR

This study shows how antibiotic-degrading bacteria influence resistance gene spread and transfer in different soil types.

Contribution

The study identifies soil-specific resistome networks and highlights the role of ADB in horizontal gene transfer.

Findings

ADB in soils carry more diverse and chromosomal ARGs, often linked to mobile genetic elements.

Soil type influences the abundance and diversity of ARG hosts and degradation bacteria.

89 ARGs or MGEs were found co-located with degradation genes, indicating strong HGT potential.

Abstract

Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied 13C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs — especially multidrug and tetracycline resistance genes — often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.

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