Distinct aggregate stratification of antibiotic resistome in farmland soil with long-term manure application

Agricultural soils, which are closely linked to human health via food supply, have been recognized as an important reservoir for antibiotic resistance genes (ARGs). However, there is still a lack of knowledge regarding the role of soil aggregates in shaping ARG profile. In this study, we collected soils from long-termexperimental farmland plots receiving inorganic and/or organic fertilizers and examined the patterns of antibiotic resistome distribution among differently sized soil aggregates using high-throughput quantitative polymerase chain reaction (HT-qPCR). Our results showed that the distribution of soil ARGs could be affected by manure application and aggregate size individually but not interactively. More diverse and abundant ARGs were found in the manured soils, compared to the non-manured soils. The aggregate size fraction of <53 mu m exhibited the highest diversity and abundance of ARGs. Variation partitioning analysis revealed that soil traits, mobile genetic elements, and bacterial community collectively contributed to the variation of soil antibiotic resistance. The knowledge about aggregation stratification of soil ARGs obtained in this study is fundamental and essential to understanding the fate of soil ARGs at the microscale.

Automated summary

Agricultural soils play a significant role in the reservoir of antibiotic resistance genes (ARGs) that are closely related to human health through the food supply. This study investigated the impact of soil aggregates on the distribution of ARGs. The results showed that manure application and aggregate size individually influenced the distribution of soil ARGs, with manured soils having more diverse and abundant ARGs. The <53 μm aggregate size fraction exhibited the highest diversity and abundance of ARGs. Soil traits, mobile genetic elements, and bacterial community collectively contributed to the variation of soil antibiotic resistance.