Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures

Land application of animal manures is a major dissemination route for antibiotic resistance genes (ARGs) in agro-ecosystems, which are a potential risk to public health if they migrate into the food chain. Despite the fact that animal manure is a rich reservoir of ARGs our knowledge of the impacts of different types and amounts of animal manures on the temporal succession of a wide array of ARGs and potential ARG-hosts remains limited. Here, we constructed soil microcosms amended with two levels of swine, poultry or cattle manures to explore the time-course patterns of ARGs, mobile genetic elements (MGEs) including integrons and transposons, and bacterial communities. The high-throughput quantitative PCR detected 260 unique ARGs, and the application of all manure types, especially at the higher concentration (80 mg manure g(-1) soil), significantly increased the diversity and abundances of ARGs and MGEs. The abundance of ARGs in manured soils declined over time, but was still higher than that in untreated soils after 120 days, indicating the persistence of ARGs in manured soils. The next-generation sequencing revealed a clear shift in the bacterial community compositions of manured soils during the incubation. Mantel test and network analysis revealed that the ARG profile was strongly correlated with the bacterial community compositions. Variation partitioning analysis, and structure equation models, further indicated that bacterial phylogeny played a primary role in shaping the ARG profiles in manured soils. However, the significant correlation between the abundances of MGEs and ARGs suggested that the potential effects of horizontal gene transfer on the persistence of ARGs should not be overlooked. In addition, soil properties, which were strongly affected by the added manures, could also affect the ARG patterns. These findings demonstrated the temporal patterns and dissemination risk of ARGs in manured soils, which might contribute to the development of effective strategies to minimise the spread of ARGs in agro-ecosystems.