Abstract
Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one of the primary areas of intensive agriculture in China. High-throughput quantitative PCR and sequencing technologies were employed to assess the effects of long-term manure or chemical fertilizer application on the distribution of ARGs and microbial communities. A total of 114 unique ARGs were successfully amplified from all soil samples. Manure application markedly increased the relative abundance and detectable numbers of ARGs, with up to 0.23 copies/16S rRNA gene and 81 unique ARGs. The increased abundance of ARGs in manure-fertilized soil was mainly due to the manure increasing the abundance of indigenous soil ARGs. In contrast, chemical fertilizers only moderately affected the diversity of ARGs and had no significant effect on the relative abundance of the total ARGs. In addition, manure application increased the abundance of mobile genetic elements (MGEs), which were significantly and positively correlated with most types of ARGs, indicating that horizontal gene transfer via MGEs may play an important role in the spread of ARGs. Furthermore, the application of manure and chemical fertilizers significantly affected microbial community structure, and variation partitioning analysis showed that microbial community shifts represented the major driver shaping the antibiotic resistome. Taken together, our results provide insight into the long-term effects of manure and chemical fertilization on the dissemination of ARGs in intensive agricultural ecosystems.
Highlights
The increasing dissemination and propagation of antibiotic resistance genes (ARGs) in various environments has aroused great concern worldwide (Zhu et al, 2013; Fahrenfeld et al, 2014) and might threaten antibiotic effectiveness and public health in the 21st century (Berendonk et al, 2015)
Twenty-three ARGs were shared by the CK, manured soils and pig manure (PM) (Supplementary Table S5); 36 and 58 unique ARGs were detected in the M and manure and nitrogen fertilizer (MN) treatments, respectively (Figure 3C)
The principal coordinate analysis (PCoA) showed that manure application influenced the ARG composition (Supplementary Figure S4)
Summary
The increasing dissemination and propagation of antibiotic resistance genes (ARGs) in various environments has aroused great concern worldwide (Zhu et al, 2013; Fahrenfeld et al, 2014) and might threaten antibiotic effectiveness and public health in the 21st century (Berendonk et al, 2015). Manure fertilizers contain abundant nutrients and organic matter that can promote crop growth, the application of manure to farmland soils might markedly increase ARG abundance and ARB populations in soils (Heuer et al, 2011) by introducing new types of ARGs or elevating existing ARG levels (UdikovicKolic et al, 2014). In China, over 3 billion tons of livestock manure is produced each year, and most manure is applied to farmlands after no or little treatment (Wang et al, 2006; You and Silbergeld, 2014). This practice might introduce antibiotics and ARGs into soils (Qiao et al, 2012) and further spread ARGs in the soil microbial community. Considering the high levels of ARGs and ARB in manure, we still lack a comprehensive understanding of the impact of manure fertilization on the spread of ARGs in the soils of the cropping systems on the NCP
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