Land-use-dependent responses of soil antibiotic resistance to manure input under current and future climates

Antimicrobial resistance is on the rise and poses a global public health risk. Livestock manure serves as a primary source of antibiotic resistance in agricultural soils, where the specific agricultural management and climatic factors may influence antimicrobial resistance genes (ARG) levels and diversity. However, the compounded effects of climate change and shifts in land use on the spread of antibiotic resistance from livestock manure to soil microbiomes have not been studied. This study fills this knowledge gap by using soils from the “Global Change Experimental Facility” which investigates the consequences of climate change on ecosystem processes in different land-use types. Soils with four distinct land-use histories reflecting different agricultural management practices (conventional farming, organic farming, intensive grassland, and extensive grassland) were amended with cattle manure and incubated under current and future climate scenarios according to IPCC projections. The antimicrobial resistance genes (the resistome) and the mobile genetic elements (the mobilome) of the soil microbiomes were analyzed via metagenomics, while the abundance of clinically important resistance genes was quantified over time using real‑time quantitative PCR. The metagenomic approach indicates that 56% of the genes are shared among different land-use types, and a similar proportion of ARGs occurs in soils with or without manure additions. While the same ARG classes remain dominant across all treatments, the total ARG counts are consistently higher in grasslands than in croplands. Under conventional farming, future climatic conditions lead to an increase of unique ARGs, whereas organic farming maintains the same number of unique ARGs under both climatic scenarios. In intensive and extensive meadows, future climatic conditions show an increase of the unique ARGs compared to current ambient conditions. The temporal evaluation across all treatments revealed an overall decrease in the counts of the main ARG classes, such that, four months after manure addition, ARG abundances closely resembled the natural levels observed in soils without manure application and a similar ARGs composition. Overall, agricultural management was the main determinant of total ARG abundance, whereas future climatic conditions primarily influenced the occurrence of unique ARGs in a land-use-dependent manner.