Soil management strategies drive divergent impacts on pathogens and environmental resistomes

This large field study examined how different soil management practices influence the spread of antimicrobial resistance (AMR) genes after manure is applied to farmland. Although livestock manure is known to contain AMR genes, the researchers found that non-organic farming practices—despite not using poultry manure—actually posed a greater risk for transmitting AMR genes and human pathogens. This was because non-organic soils showed a much higher co-occurrence of resistance genes with mobile genetic elements, which enable bacteria to share resistance traits more easily. Organic soils that received composted poultry manure did contain more AMR and metal-resistance genes overall, but these genes were less diverse and far less mobile, meaning they were less likely to spread. The study shows that measuring only the abundance of resistance genes can give a misleading picture of AMR risk; gene mobility and the broader management context matter greatly. These findings highlight how smarter soil management can help reduce the environmental spread of AMR and support more sustainable and healthier agricultural systems.