Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment

The increasing emergence of antibiotic-resistant genes (ARGs) represents a global threat to human health. Land application of animal manure is known to contribute considerably to the propagation and dispersal of antibiotic resistance in agro-ecosystems. Yet, the primary determinants of the fate of the soil resistome remain obscure. In this study, a pot experiment was conducted to examine temporal changes in ARGs, mobile genetic elements (MGEs), and bacterial communities in a weakly developed loamy soil (an entisol known as calcareous purple soil) upon addition of pig or chicken manure. On the day of manure application, substantial increases in the diversity and relative abundance of ARGs were observed in soil amended with raw pig manure. At the same time, no obvious changes were observed for soil amended with chicken manure. Antibiotic resistance in pig manure-amended soils rapidly decreased over time to a level that was still higher than that of unamended soil at 100 days after manure application. The results of the Mantel test and Procrustes analysis indicated that ARG profiles in soil were significantly correlated with the structure of the bacterial phylogeny. Variation partitioning analysis further revealed that the bacterial community played a major role in regulating the temporal changes in ARGs in soil following manure application. Increased numbers and relative abundances of MGEs and their significant positive correlations with ARGs were observed, which suggest that a potential contribution from lateral gene transfer to the persistence and spread of ARGs should not be overlooked. Overall, our findings provide a better understanding of the mechanisms underlying the dynamics of ARGs in entisols following manure application and have practical implications for managing manure applications in entisols of the study area and other areas.