Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4%) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture. Organic fertilizers potentiate the proliferation of antibiotic resistance in farmland. However, little is known about how bacterial antibiotic resistance evolve in fertilized soils, and even spread to crops. We finely delineated the dynamic evolution of the antibiotic resistome in farmlands under different fertilization practices during crop growth and revealed the decision-making process underlying the evolution of resistance. Then, we identified key drivers and investigated their effects on bacterial antibiotic resistance in terms of plasmid persistence and conjugation transfer. The results of this study will provide comprehensive and in-depth insights into the occurrence, adaptation, and persistence of bacterial resistance in farmlands.